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
Q6AYK4 UniProt NPD GO	B2L14_RAT	Apoptosis facilitator Bcl-2-like protein 14	0.49	-	nuc	0	Cytoplasm (By similarity)				326
Q400G9 UniProt NPD GO	AMZ1_HUMAN	Archaemetzincin-1 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 1)	0.49	-	nuc	0					498
Q3UZB0 UniProt NPD GO	ARMX5_MOUSE	Armadillo repeat-containing X-linked protein 5	0.49	-	nuc	0					606
P08290 UniProt NPD GO	ASGR2_RAT	Asialoglycoprotein receptor 2 (ASGP-R 2) (ASGPR 2) (Hepatic lectin R2/3) (RHL-2)	0.49	-	mit	1	Membrane; single-pass type II membrane protein				301
O75882 UniProt NPD GO	ATRN_HUMAN	Attractin precursor (Mahogany homolog) (DPPT-L)	0.49	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3, isoform 4, isof ...	extracellular space [TAS] integral to plasma membrane [TAS] plasma membrane [NAS]	603130		1429
Q5AZC0 UniProt NPD GO	ATG17_EMENI	Autophagy-related protein 17	0.49	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				588
Q756Z7 UniProt NPD GO	ATG23_ASHGO	Autophagy-related protein 23	0.49	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				407
Q59AF4 UniProt NPD GO	IAA4_ORYSA	Auxin-responsive protein IAA4 (Indoleacetic acid-induced protein 4)	0.49	-	nuc	0	Nucleus (By similarity)				203
P02849 UniProt NPD GO	BAR1_CHITE	Balbiani ring protein 1 (Giant secretory protein I-A) (GSP-IA) (Fragment)	0.49	-	nuc	0	Secreted protein				174
O88498 UniProt NPD GO	BIM_RAT	Bcl-2-like protein 11 (Bcl2-interacting mediator of cell death) (Bcl-2-related ovarian death protein ...	0.49	-	nuc	0	Membrane; peripheral membrane protein. Associated with intracytoplasmic membranes (By similarity)				196
O55102 UniProt NPD GO	BL1S1_MOUSE	Biogenesis of lysosome-related organelles complex-1 subunit 1 (BLOC-1 subunit 1) (GCN5-like protein ...	0.49	-	nuc	0		cytosol [IDA]			125
Q7Z5Y6 UniProt NPD GO	BMP8A_HUMAN	Bone morphogenetic protein 8A precursor (BMP-8A)	0.49	-	end	0	Secreted protein				402
P34821 UniProt NPD GO	BMP8A_MOUSE	Bone morphogenetic protein 8A precursor (BMP-8A) (Osteogenic protein 2) (OP-2)	0.49	+	vac	0	Secreted protein (By similarity)				399
Q9N3F0 UniProt NPD GO	BXDC1_CAEEL	Brix domain-containing protein 1 homolog	0.49	+	nuc	0	Nucleus; nucleolus (By similarity)				297
P60883 UniProt NPD GO	CD209_CERAE	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.49	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				381
Q8HXZ8 UniProt NPD GO	CD209_GORGO	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.49	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				427
Q8HY03 UniProt NPD GO	CD209_HYLLA	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.49	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				450
Q95J96 UniProt NPD GO	CD209_MACMU	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.49	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				404
Q95LC6 UniProt NPD GO	CD209_MACNE	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1)	0.49	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				381
Q15762 UniProt NPD GO	CD226_HUMAN	CD226 antigen precursor (DNAX accessory molecule 1) (DNAM-1)	0.49	+	mit	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	605397		336
Q9VGZ1 UniProt NPD GO	CK5P1_DROME	CDK5RAP1-like protein	0.49	-	mit	0					583
Q4IMN9 UniProt NPD GO	CSN12_GIBZE	COP9 signalosome complex subunit 12	0.49	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				502
Q9TTR8 UniProt NPD GO	COT1_BOVIN	COUP transcription factor 1 (COUP-TF1) (COUP-TF I)	0.49	-	nuc	0	Nucleus (Potential)				424
P24468 UniProt NPD GO	COT2_HUMAN	COUP transcription factor 2 (COUP-TF2) (COUP-TF II) (Apolipoprotein AI regulatory protein 1) (ARP-1) ...	0.49	-	nuc	0	Nucleus	nucleus [TAS]	107773		414
P43135 UniProt NPD GO	COT2_MOUSE	COUP transcription factor 2 (COUP-TF2) (COUP-TF II) (Apolipoprotein AI regulatory protein 1) (ARP-1) ...	0.49	-	nuc	0	Nucleus	nucleus [IDA]			414
Q9ULB4 UniProt NPD GO	CADH9_HUMAN	Cadherin-9 precursor	0.49	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			789
Q01064 UniProt NPD GO	PDE1B_HUMAN	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17) (Cam-PDE 1B) ...	0.49	-	mit	0	Cytoplasm		171891	1TAZ	536
Q9GLG1 UniProt NPD GO	CAN2_MACFA	Calpain-2 catalytic subunit precursor (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated ne ...	0.49	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				699
Q03792 UniProt NPD GO	RIM13_YEAST	Calpain-like protease 1 (EC 3.4.22.-) (Cysteine protease RIM13) (Calpain-7) (Regulator of IME2 prote ...	0.49	-	nuc	0					727
P11012 UniProt NPD GO	CALR_ONCVO	Calreticulin precursor (RAL1 antigen) (Protein ral-1) (41 kDa larval antigen)	0.49	+	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				388
Q8VI47 UniProt NPD GO	MRP2_MOUSE	Canalicular multispecific organic anion transporter 1 (ATP-binding cassette sub-family C member 2)	0.49	+	end	16 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] integral to plasma membrane [IDA] intercellular canaliculus [IDA]			1543
Q60HG9 UniProt NPD GO	CPT2_MACFA	Carnitine O-palmitoyltransferase 2, mitochondrial precursor (EC 2.3.1.21) (Carnitine palmitoyltransf ...	0.49	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				658
Q66K08 UniProt NPD GO	CILP1_MOUSE	Cartilage intermediate layer protein 1 precursor (CILP-1) [Contains: Cartilage intermediate layer pr ...	0.49	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1184
P40236 UniProt NPD GO	HHP2_SCHPO	Casein kinase I homolog hhp2 (EC 2.7.11.1)	0.49	-	nuc	0	Nucleus (Probable)				400
Q9GKT0 UniProt NPD GO	ATCAY_MACFA	Caytaxin	0.49	-	cyt	2					371
P32468 UniProt NPD GO	CDC12_YEAST	Cell division control protein 12 (Septin)	0.49	-	cyt	0	Membrane; peripheral membrane protein. Bud neck. Present at the bud neck during cell division. Proba ...	cytoplasm [IDA] septin ring (sensu Saccharomyces) [TAS]			407
Q01917 UniProt NPD GO	CDC2H_CRIFA	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.49	-	nuc	0					474
P54609 UniProt NPD GO	CD48A_ARATH	Cell division control protein 48 homolog A (AtCDC48a)	0.49	-	cyt	0	Nucleus. Phragmoplast. Primarily localized to the nucleus and, during cytokinesis, to the phragmopla ...				809
Q9LZF6 UniProt NPD GO	CD48E_ARATH	Cell division control protein 48 homolog E (AtCDC48e) (Transitional endoplasmic reticulum ATPase E)	0.49	-	cyt	0	Nucleus (By similarity). Phragmoplast (By similarity). Primarily localized to the nucleus and, durin ...				810
P20911 UniProt NPD GO	CDK7_XENLA	Cell division protein kinase 7 (EC 2.7.11.22) (EC 2.7.11.23) (40 kDa protein kinase) (P40 MO15) (CDC ...	0.49	-	mit	0	Nucleus. In the prominent nucleus of oocytes				352
Q6GLD8 UniProt NPD GO	CDK9_XENTR	Cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9)	0.49	-	cyt	0	Nucleus (By similarity)				376
Q09854 UniProt NPD GO	MOK11_SCHPO	Cell wall alpha-1,3-glucan synthase mok11 (EC 2.4.1.183)	0.49	-	end	13					2397
P79734 UniProt NPD GO	P53_BRARE	Cellular tumor antigen p53 (Tumor suppressor p53)	0.49	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				373
Q7YW31 UniProt NPD GO	CTR1_OCTVU	Cephalotocin receptor 1 (OT/VP superfamily peptide receptor 1) (OC/CE-R 1)	0.49	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IC]			397
O95833 UniProt NPD GO	CLIC3_HUMAN	Chloride intracellular channel protein 3	0.49	-	cyt	0	Nucleus. Predominantly. Cytoplasm. Some protein was found in the cytoplasm	cytoplasm [IDA] nucleus [IDA]	606533		236
P19460 UniProt NPD GO	RR10_GUITH	Chloroplast 30S ribosomal protein S10	0.49	-	nuc	0	Plastid; chloroplast				102
Q9BA08 UniProt NPD GO	RR15_OENHO	Chloroplast 30S ribosomal protein S15	0.49	-	nuc	0	Plastid; chloroplast				87
Q6H9L6 UniProt NPD GO	RR4_EQUAR	Chloroplast 30S ribosomal protein S4	0.49	-	nuc	0	Plastid; chloroplast				207
Q6H9L3 UniProt NPD GO	RR4_EQUFL	Chloroplast 30S ribosomal protein S4	0.49	-	nuc	0	Plastid; chloroplast				207
Q6H9L2 UniProt NPD GO	RR4_EQUGI	Chloroplast 30S ribosomal protein S4	0.49	-	nuc	0	Plastid; chloroplast				207

You are viewing entries 25451 to 25500 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.