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
P28653 UniProt NPD GO	PGS1_MOUSE	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1)	0.18	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				369
P07738 UniProt NPD GO	PMGE_HUMAN	Bisphosphoglycerate mutase (EC 5.4.2.4) (2,3-bisphosphoglycerate mutase, erythrocyte) (2,3-bisphosph ...	0.18	-	cyt	0			222800	1T8P	258
P15327 UniProt NPD GO	PMGE_MOUSE	Bisphosphoglycerate mutase (EC 5.4.2.4) (2,3-bisphosphoglycerate mutase, erythrocyte) (2,3-bisphosph ...	0.18	-	cyt	0					258
P01055 UniProt NPD GO	IBB1_SOYBN	Bowman-Birk type proteinase inhibitor precursor (BBI)	0.18	-	exc	0				2BBI	110
Q6UXE8 UniProt NPD GO	BTNL3_HUMAN	Butyrophilin-like protein 3 precursor (Butyrophilin-like receptor)	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606192		466
P51676 UniProt NPD GO	CC1L1_MOUSE	C-C chemokine receptor 1-like protein 1 (Macrophage inflammatory protein 1 alpha receptor-like 1)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				356
Q9TV42 UniProt NPD GO	CCR5_CERPY	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.18	-	end	6 *	Membrane; multi-pass membrane protein				352
P61072 UniProt NPD GO	CXCR4_PANTR	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.18	-	end	7 *	Membrane; multi-pass membrane protein				352
P61073 UniProt NPD GO	CXCR4_HUMAN	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (Stromal cell-derived factor 1 receptor) (SDF-1 re ...	0.18	-	end	7 *	Membrane; multi-pass membrane protein		193670		352
O19910 UniProt NPD GO	PHCA_CYACA	C-phycocyanin alpha chain	0.18	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome rod				162
Q9W758 UniProt NPD GO	CTBPB_XENLA	C-terminal-binding protein B (TCF-3 corepressor CtBP) (XCtBP)	0.18	+	nuc	0	Nucleus (Potential)				437
Q9JKF4 UniProt NPD GO	CLC6A_MOUSE	C-type lectin domain family 6 member A (C-type lectin superfamily member 10) (Dendritic cell-associa ...	0.18	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				209
Q63514 UniProt NPD GO	C4BP_RAT	C4b-binding protein alpha chain precursor (C4bp)	0.18	-	nuc	0					558
Q8N6Q3 UniProt NPD GO	CD177_HUMAN	CD177 antigen precursor (Polycythemia rubra vera protein 1) (PRV-1) (NB1 glycoprotein) (NB1 GP) (Hum ...	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor		162860		437
Q01151 UniProt NPD GO	CD83_HUMAN	CD83 antigen precursor (Cell surface protein HB15) (B-cell activation protein)	0.18	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604534		205
Q8VCN6 UniProt NPD GO	CD99_MOUSE	CD99 antigen precursor (Paired immunoglobin-like type 2 receptor-ligand) (PILR-L)	0.18	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				175
Q9DAR1 UniProt NPD GO	CLF2A_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 2A (Chemokine-like factor superfamily membe ...	0.18	-	end	4 *	Membrane; multi-pass membrane protein	cytoplasm [IDA] nucleus [IPI]			169
P54751 UniProt NPD GO	SIA4A_MOUSE	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.4) (Beta-galactosi ...	0.18	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				337
Q11201 UniProt NPD GO	SIA4A_HUMAN	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.4) (Beta-galactosi ...	0.18	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...		607187		340
Q8TDQ1 UniProt NPD GO	CLM1_HUMAN	CMRF35-like-molecule 1 precursor (CLM-1) (Immune receptor expressed on myeloid cells protein 1) (IRE ...	0.18	-	end	1	Membrane; single-pass type I membrane protein (Potential)		609807		290
P68355 UniProt NPD GO	CSN5B_BRAOL	COP9 signalosome complex subunit 5b (EC 3.4.-.-) (Signalosome subunit 5b) (Jun activation domain-bin ...	0.18	-	nuc	0	Cytoplasm. Nucleus				78
Q9UJ99 UniProt NPD GO	CAD22_HUMAN	Cadherin-22 precursor (Pituitary and brain cadherin) (PB-cadherin)	0.18	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)		609920		828
P55286 UniProt NPD GO	CADH8_HUMAN	Cadherin-8 precursor	0.18	-	nuc	1 *	Membrane; single-pass type I membrane protein		603008		799
P30988 UniProt NPD GO	CALCR_HUMAN	Calcitonin receptor precursor (CT-R)	0.18	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	114131		490
Q96Q77 UniProt NPD GO	KIP3_HUMAN	Calcium and integrin-binding protein 3 (Kinase-interacting protein 3) (KIP 3)	0.18	-	nuc	0					187
Q9N1Q9 UniProt NPD GO	CABP2_BOVIN	Calcium-binding protein 2 (CaBP2)	0.18	-	nuc	0					162
Q9Y2V2 UniProt NPD GO	CHSP1_HUMAN	Calcium-regulated heat stable protein 1 (Calcium-regulated heat-stable protein of 24 kDa) (CRHSP-24) ...	0.18	-	nuc	0	Cytoplasm (By similarity)				147
Q9CR86 UniProt NPD GO	CHSP1_MOUSE	Calcium-regulated heat stable protein 1 (Calcium-regulated heat-stable protein of 24 kDa) (CRHSP-24) ...	0.18	-	nuc	0	Cytoplasm (By similarity)				148
Q61481 UniProt NPD GO	PDE1A_MOUSE	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A (EC 3.1.4.17) (Cam-PDE 1A) ...	0.18	-	cyt	0					565
P22517 UniProt NPD GO	KCC2_YEAST	Calcium/calmodulin-dependent protein kinase II (EC 2.7.11.17)	0.18	-	cyt	0		cytoplasm [IDA]			447
Q96L46 UniProt NPD GO	CPNS2_HUMAN	Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)	0.18	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon c ...				248
Q9DAW9 UniProt NPD GO	CNN3_MOUSE	Calponin-3 (Calponin, acidic isoform)	0.18	-	nuc	0					330
P29413 UniProt NPD GO	CALR_DROME	Calreticulin precursor (CRP55) (Calregulin) (HACBP)	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				406
Q9H4D0 UniProt NPD GO	CSTN2_HUMAN	Calsyntenin-2 precursor	0.18	-	end	1	Membrane; single-pass type I membrane protein (Potential)				955
P54213 UniProt NPD GO	CATR_DUNSA	Caltractin (Centrin)	0.18	-	nuc	0					169
P53441 UniProt NPD GO	CATR_NAEGR	Caltractin (Centrin)	0.18	-	nuc	0	Centrosome. Centrosome of interphase and mitotic cells				172
O19886 UniProt NPD GO	CARA_CYACA	Carbamoyl-phosphate synthase small chain (EC 6.3.5.5) (Carbamoyl-phosphate synthetase glutamine chai ...	0.18	-	cyt	0	Plastid; chloroplast				399
Q6PGK7 UniProt NPD GO	CHSTA_MOUSE	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST)	0.18	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
Q9MZ30 UniProt NPD GO	CAH12_RABIT	Carbonic anhydrase 12 precursor (EC 4.2.1.1) (Carbonic anhydrase XII) (Carbonate dehydratase XII) (C ...	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				355
Q99N23 UniProt NPD GO	CAH15_MOUSE	Carbonic anhydrase 15 precursor (EC 4.2.1.1) (Carbonic anhydrase XV) (Carbonate dehydratase XV) (CA- ...	0.18	-	cyt	0	Secreted protein (Potential)				324
O14595 UniProt NPD GO	CTDS2_HUMAN	Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 (EC 3.1.3.16) (Small CTD ...	0.18	-	cyt	0	Nucleus (Potential)	soluble fraction [TAS]	608711		271
Q6P8K8 UniProt NPD GO	CBPA4_MOUSE	Carboxypeptidase A4 precursor (EC 3.4.17.-)	0.18	-	cyt	0	Secreted protein (By similarity)				420
Q8WXQ8 UniProt NPD GO	CBPA5_HUMAN	Carboxypeptidase A5 precursor (EC 3.4.17.1)	0.18	-	mit	0	Secreted protein (By similarity)		609561		436
O89001 UniProt NPD GO	CBPD_MOUSE	Carboxypeptidase D precursor (EC 3.4.17.22) (Metallocarboxypeptidase D) (gp180)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				1377
Q9JHW1 UniProt NPD GO	CBPD_RAT	Carboxypeptidase D precursor (EC 3.4.17.22) (Metallocarboxypeptidase D) (gp180)	0.18	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Nucleus	Golgi trans face [IPI] integral to membrane [ISS] microsome [IPI] nucleus [IDA]			1378
P26677 UniProt NPD GO	PPLA_CHICK	Cardiac phospholamban (PLB)	0.18	-	mit	1 *	Membrane				52
Q8TG13 UniProt NPD GO	CSK2A_NEUCR	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II subunit alpha)	0.18	-	cyt	0					336
Q9CWL2 UniProt NPD GO	CASZ1_MOUSE	Castor homolog 1 zinc finger protein (Castor-related protein) (Fragment)	0.18	-	nuc	0	Nucleus (Probable)				255
P58781 UniProt NPD GO	CECR1_BRARE	Cat eye syndrome critical region protein 1 homolog precursor	0.18	-	nuc	0					503
Q9NZK5 UniProt NPD GO	CECR1_HUMAN	Cat eye syndrome critical region protein 1 precursor	0.18	-	nuc	1 *			607575		511

You are viewing entries 52801 to 52850 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.