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
Q24451 UniProt NPD GO	MAN2_DROME	Alpha-mannosidase 2 (EC 3.2.1.114) (Alpha-mannosidase II) (Mannosyl-oligosaccharide 1,3-1,6-alpha-ma ...	0.70	+	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	endoplasmic reticulum [NAS] Golgi stack [NAS]		1TQW	1108
Q9LXZ5 UniProt NPD GO	SNAA1_ARATH	Alpha-soluble NSF attachment protein 1 (Alpha-SNAP1) (N-ethylmaleimide-sensitive factor attachment p ...	0.70	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				381
Q6DCV1 UniProt NPD GO	AB1IP_XENLA	Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (APBB1-interacting p ...	0.70	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity)				653
Q86YJ7 UniProt NPD GO	AN13B_HUMAN	Ankyrin repeat domain-containing protein 13B	0.70	-	nuc	0					626
P07355 UniProt NPD GO	ANXA2_HUMAN	Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) ...	0.70	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...	plasma membrane [TAS] soluble fraction [TAS]	151740	1XJL	338
P35207 UniProt NPD GO	SKI2_YEAST	Antiviral helicase SKI2 (EC 3.6.1.-)	0.70	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleolus [TAS]			1287
P26442 UniProt NPD GO	AMFR1_HUMAN	Autocrine motility factor receptor precursor, isoform 1 (AMF receptor)	0.70	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	603243		323
Q75E74 UniProt NPD GO	ATG2_ASHGO	Autophagy-related protein 2	0.70	-	cyt	0	Perivacuolar compartment (By similarity)				1525
Q3LRP3 UniProt NPD GO	CD19_CALJA	B-lymphocyte antigen CD19 precursor (Differentiation antigen CD19)	0.70	+	exc	1	Membrane; single-pass type I membrane protein (By similarity)				558
Q8N1M1 UniProt NPD GO	VMDL3_HUMAN	Bestrophin-4 (Vitelliform macular dystrophy 2-like protein 3)	0.70	-	end	4 *	Cell membrane; multi-pass membrane protein		607337		668
P06651 UniProt NPD GO	BIND_STRPU	Bindin precursor	0.70	-	exc	0	Acrosome; acrosomal lumen				481
P21274 UniProt NPD GO	BMP2_MOUSE	Bone morphogenetic protein 2 precursor (BMP-2) (BMP-2A)	0.70	+	exc	1 *	Secreted protein	extracellular space [IDA]			394
P55108 UniProt NPD GO	BMP3B_RAT	Bone morphogenetic protein 3b precursor (BMP-3b) (Growth/differentiation factor 10) (GDF-10) (Bone-i ...	0.70	+	exc	0	Secreted protein				476
Q8BKX1 UniProt NPD GO	BAIP2_MOUSE	Brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) (BAI-associ ...	0.70	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Detected throughou ...				535
Q5R7Y0 UniProt NPD GO	BAI2_PONPY	Brain-specific angiogenesis inhibitor 2 precursor	0.70	-	end	6	Membrane; multi-pass membrane protein				1485
Q9Y6D6 UniProt NPD GO	BIG1_HUMAN	Brefeldin A-inhibited guanine nucleotide-exchange protein 1 (Brefeldin A-inhibited GEP 1) (p200 ARF- ...	0.70	-	nuc	0			604141		1849
Q8BUG5 UniProt NPD GO	CAYP2_MOUSE	Calcyphosin-2 (Calcyphosine-2)	0.70	-	nuc	0					550
Q9D3A8 UniProt NPD GO	CAPON_MOUSE	Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein (C--terminal PDZ ligand of ne ...	0.70	+	nuc	0					503
P40235 UniProt NPD GO	HHP1_SCHPO	Casein kinase I homolog hhp1 (EC 2.7.11.1)	0.70	-	nuc	0	Nucleus (Probable)				365
Q09884 UniProt NPD GO	DCR1_SCHPO	Cell cycle control protein dcr1 (EC 3.6.1.-) (ATP-dependent helicase dcr1) (RNA interference pathway ...	0.70	-	cyt	0					1374
P40986 UniProt NPD GO	CDC1_YEAST	Cell division control protein 1	0.70	-	nuc	3 *					491
Q10990 UniProt NPD GO	CDT2_SCHPO	Cell division cycle protein cdt2	0.70	-	nuc	0	Nucleus	nucleus [IDA]			490
P53832 UniProt NPD GO	WSC2_YEAST	Cell wall integrity and stress response component 2 precursor	0.70	-	exc	1		cytoplasm [IDA] site of polarized growth [IDA]			503
O74684 UniProt NPD GO	KNH1_CANGA	Cell wall synthesis protein KNH1 precursor	0.70	+	exc	0	Cell surface (By similarity). Secreted, probably found at cell surface (By similarity)				265
Q9BY43 UniProt NPD GO	CHM4A_HUMAN	Charged multivesicular body protein 4a (Chromatin-modifying protein 4a) (CHMP4a) (Vacuolar protein s ...	0.70	-	nuc	0	Cytoplasmic vesicle. Membrane-associated. Localizes to large vesicle-like structures				222
P40955 UniProt NPD GO	CHS6_YEAST	Chitin biosynthesis protein CHS6 (Protein CSD3)	0.70	-	nuc	0					746
Q5SD37 UniProt NPD GO	RR18_HUPLU	Chloroplast 30S ribosomal protein S18	0.70	-	nuc	0	Plastid; chloroplast				81
Q32RN8 UniProt NPD GO	RK2_ZYGCR	Chloroplast 50S ribosomal protein L2	0.70	-	nuc	0	Plastid; chloroplast				277
Q68RY3 UniProt NPD GO	RK20_PANGI	Chloroplast 50S ribosomal protein L20	0.70	-	mit	0	Plastid; chloroplast				128
P45895 UniProt NPD GO	CHSS2_CAEEL	Chondroitin sulfate synthase 2 (EC 2.4.1.175) (Chondroitin-polymerizing factor S) (N-acetylgalactosa ...	0.70	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				804
Q5KL22 UniProt NPD GO	VID21_CRYNE	Chromatin modification-related protein VID21	0.70	+	nuc	0	Nucleus (Probable)				985
P32074 UniProt NPD GO	COPG_YEAST	Coatomer subunit gamma (Gamma-coat protein) (Gamma-COP)	0.70	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			935
Q66HA5 UniProt NPD GO	CC21A_RAT	Coiled-coil and C2 domain-containing protein 1A (Five repressor element under dual repression-bindin ...	0.70	-	nuc	0	Cytoplasm. Nucleus				941
Q4ADK4 UniProt NPD GO	CFDP1_MUNRE	Craniofacial development protein 1 (Bucentaur)	0.70	-	nuc	0					298
Q60FC2 UniProt NPD GO	CFDP1_TRAJA	Craniofacial development protein 1 (Bucentaur) (h-type BCNT protein)	0.70	-	nuc	0					298
Q6SLL5 UniProt NPD GO	CDN1B_CANFA	Cyclin-dependent kinase inhibitor 1B (Cyclin-dependent kinase inhibitor p27) (p27Kip1)	0.70	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear and cytoplasmic in quiescent cells. Upon ...				198
P49919 UniProt NPD GO	CDN1C_MOUSE	Cyclin-dependent kinase inhibitor 1C (Cyclin-dependent kinase inhibitor p57) (p57KIP2)	0.70	-	nuc	0	Nucleus	nucleus [IDA]			348
Q4R7T5 UniProt NPD GO	CDKL2_MACFA	Cyclin-dependent kinase-like 2 (EC 2.7.11.22)	0.70	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				570
Q76MZ1 UniProt NPD GO	CYH1_CERAE	Cytohesin-1	0.70	-	cyt	0					398
Q15438 UniProt NPD GO	CYH1_HUMAN	Cytohesin-1 (SEC7 homolog B2-1)	0.70	-	cyt	0		cytoplasm [IDA] plasma membrane [IDA]	182115	1BC9	398
O08967 UniProt NPD GO	CYH3_MOUSE	Cytohesin-3 (ARF nucleotide-binding site opener 3) (ARNO3 protein) (General receptor of phosphoinosi ...	0.70	+	cyt	0		cytoplasm [IDA] plasma membrane [IDA] ruffle [IPI]		1U2B	399
Q8TD16 UniProt NPD GO	BICD2_HUMAN	Cytoskeleton-like bicaudal D protein homolog 2	0.70	-	nuc	0	Golgi apparatus. In interphase cells mainly localizes to the Golgi complex and colocalizes with dyna ...		609797		824
Q50L43 UniProt NPD GO	PA24D_MOUSE	Cytosolic phospholipase A2 delta (EC 3.1.1.4) (cPLA2-delta) (Phospholipase A2 group IVD)	0.70	-	cyt	0	Cytoplasm; cytosol. Translocates to membrane vesicles in a calcium-dependent fashion. Translocates t ...	cytoplasm [IDA]			825
Q50L41 UniProt NPD GO	PA24F_MOUSE	Cytosolic phospholipase A2 zeta (EC 3.1.1.4) (cPLA2-zeta) (Phospholipase A2 group IVF)	0.70	-	cyt	0	Cytoplasm; cytosol. Translocates to lysosomal membranes in a calcium-dependent fashion	cytoplasm [IDA]			855
Q8CCA0 UniProt NPD GO	DCNL4_MOUSE	DCN1-like protein 4 (Defective in cullin neddylation protein 1-like protein 4) (DCUN1 domain-contain ...	0.70	+	cyt	0					292
P39009 UniProt NPD GO	DUN1_YEAST	DNA damage response protein kinase DUN1 (EC 2.7.11.1)	0.70	-	nuc	0	Nucleus	nucleus [IDA]			513
P09838 UniProt NPD GO	TDT_MOUSE	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.70	-	cyt	0	Isoform TDT-S: Nucleus. Isoform TDT-L: Cytoplasm	nucleus [TAS]		1KEJ	530
P05468 UniProt NPD GO	DPO2_KLULA	DNA polymerase (EC 2.7.7.7) (Plasmid PGKL-2 protein 2)	0.70	-	nuc	0					994
P24482 UniProt NPD GO	DPB2_YEAST	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.70	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] epsilon DNA polymerase complex [IDA] nucleus [IDA] replication fork [TAS]			689
Q9USX3 UniProt NPD GO	RAD60_SCHPO	DNA repair protein rad60	0.70	-	nuc	0	Nucleus	nucleus [IDA]			406

You are viewing entries 13651 to 13700 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.