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
Q9NYQ6 UniProt NPD GO	CELR1_HUMAN	Cadherin EGF LAG seven-pass G-type receptor 1 precursor (Flamingo homolog 2) (hFmi2)	0.41	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604523		3014
Q9CZM9 UniProt NPD GO	KCMB2_MOUSE	Calcium-activated potassium channel subunit beta 2 (Calcium-activated potassium channel, subfamily M ...	0.41	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)				235
P35085 UniProt NPD GO	CBPA_DICDI	Calcium-binding protein	0.41	-	nuc	0					467
Q06138 UniProt NPD GO	CAB39_MOUSE	Calcium-binding protein 39 (Protein Mo25)	0.41	-	cyt	0	Cytoplasm (Potential)				341
Q24210 UniProt NPD GO	CAKI_DROME	Calcium/calmodulin-dependent protein kinase (EC 2.7.11.17) (CAKI) (Peripheral plasma membrane protei ...	0.41	-	cyt	0					898
Q28068 UniProt NPD GO	CALI_BOVIN	Calicin	0.41	-	cyt	0	Calyx. Sperm head cytoskeletal structure tightly associated to the nucleus	cytoskeleton [IDA]			588
Q92178 UniProt NPD GO	CAN2_CHICK	Calpain-2 catalytic subunit precursor (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated ne ...	0.41	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				699
O42779 UniProt NPD GO	CARP9_CANAL	Candidapepsin-9 precursor (EC 3.4.23.24) (Aspartate protease 9) (ACP 9) (Secreted aspartic protease ...	0.41	-	exc	0	Secreted protein				544
Q2VEX9 UniProt NPD GO	CRTSO_DAUCA	Carotenoid isomerase, chloroplast precursor (EC 5.-.-.-) (CrtISO)	0.41	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (By similarity)				615
P08181 UniProt NPD GO	CSK2A_DROME	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II alpha subunit)	0.41	-	nuc	0		cytosol [IDA] nucleus [IDA] protein kinase CK2 complex [IDA]			335
P28020 UniProt NPD GO	CSK22_XENLA	Casein kinase II subunit alpha' (EC 2.7.11.1) (CK II)	0.41	-	mit	0					392
Q8K3Z0 UniProt NPD GO	CAR15_MOUSE	Caspase recruitment domain-containing protein 15 (Protein Nod2)	0.41	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS] cytosol [ISS] plasma membrane [ISS] vesicle [ISS]			1020
Q6WBX7 UniProt NPD GO	RAD9B_MOUSE	Cell cycle checkpoint control protein RAD9B homolog (RAD9 homolog B) (mRAD9B)	0.41	-	cyt	0					403
P51952 UniProt NPD GO	CDK7_RAT	Cell division protein kinase 7 (EC 2.7.11.22) (EC 2.7.11.23) (CDK-activating kinase) (CAK) (TFIIH ba ...	0.41	-	mit	0	Nucleus (By similarity)	cyclin-dependent protein kinase holoenzyme ... [TAS]			329
P43121 UniProt NPD GO	MUC18_HUMAN	Cell surface glycoprotein MUC18 precursor (Melanoma-associated antigen MUC18) (Melanoma cell adhesio ...	0.41	-	exc	1	Membrane; single-pass type I membrane protein	plasma membrane [NAS]	155735		646
Q9JK15 UniProt NPD GO	CENA2_RAT	Centaurin-alpha 2	0.41	-	mit	0	Cytoplasm (By similarity). Cell membrane (By similarity). Constitutively associated with the plasma ...	cytoplasm [ISS] mitochondrial envelope [IDA] plasma membrane [ISS]			376
P09232 UniProt NPD GO	PRTB_YEAST	Cerevisin precursor (EC 3.4.21.48) (Vacuolar protease B) (Proteinase YSCB)	0.41	+	nuc	0	Vacuole. Lysosome-like vacuoles	vacuolar lumen (sensu Fungi) [TAS]			635
Q5RAV2 UniProt NPD GO	CHM2B_PONPY	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b)	0.41	-	nuc	0	Cytoplasm; cytosol (By similarity)				213
Q9UQN3 UniProt NPD GO	CHM2B_HUMAN	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b) (CHMP2.5) (Vacuolar ...	0.41	-	nuc	0	Cytoplasm; cytosol		609512		213
Q9WU45 UniProt NPD GO	CLCN2_CAVPO	Chloride channel protein 2 (ClC-2)	0.41	-	end	11	Membrane; multi-pass membrane protein (Potential)				902
P51788 UniProt NPD GO	CLCN2_HUMAN	Chloride channel protein 2 (ClC-2)	0.41	-	end	12	Membrane; multi-pass membrane protein		607682		898
Q9MZT1 UniProt NPD GO	CLCN1_CANFA	Chloride channel protein, skeletal muscle (Chloride channel protein 1) (ClC-1)	0.41	-	end	11	Membrane; multi-pass membrane protein				976
Q95H53 UniProt NPD GO	RR11_WHEAT	Chloroplast 30S ribosomal protein S11	0.41	-	nuc	0	Plastid; chloroplast				143
P49500 UniProt NPD GO	RR12_ODOSI	Chloroplast 30S ribosomal protein S12	0.41	-	mit	0	Plastid; chloroplast				126
P52762 UniProt NPD GO	RR12_PINTH	Chloroplast 30S ribosomal protein S12	0.41	-	nuc	0	Plastid; chloroplast				123
P51319 UniProt NPD GO	RR14_PORPU	Chloroplast 30S ribosomal protein S14	0.41	-	nuc	0	Plastid; chloroplast				100
P06372 UniProt NPD GO	RR15_MARPO	Chloroplast 30S ribosomal protein S15	0.41	-	mit	0	Plastid; chloroplast				88
P36459 UniProt NPD GO	RR4_FESPR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.41	-	mit	0	Plastid; chloroplast				196
Q2L942 UniProt NPD GO	RR8_GOSHI	Chloroplast 30S ribosomal protein S8	0.41	-	nuc	0	Plastid; chloroplast				134
Q9MTJ0 UniProt NPD GO	RR8_OENHO	Chloroplast 30S ribosomal protein S8	0.41	-	nuc	0	Plastid; chloroplast				138
P51291 UniProt NPD GO	RR9_PORPU	Chloroplast 30S ribosomal protein S9	0.41	-	nuc	0	Plastid; chloroplast				137
P08528 UniProt NPD GO	RK16_MAIZE	Chloroplast 50S ribosomal protein L16	0.41	-	mit	0	Plastid; chloroplast				136
Q9MTI8 UniProt NPD GO	RK16_OENHO	Chloroplast 50S ribosomal protein L16	0.41	-	mit	0	Plastid; chloroplast				135
Q6L3G1 UniProt NPD GO	RK16_SACHY	Chloroplast 50S ribosomal protein L16	0.41	-	mit	0	Plastid; chloroplast				136
Q6ENS6 UniProt NPD GO	RK16_SACOF	Chloroplast 50S ribosomal protein L16	0.41	-	mit	0	Plastid; chloroplast				136
P06510 UniProt NPD GO	RK16_SPIOG	Chloroplast 50S ribosomal protein L16	0.41	-	mit	0	Plastid; chloroplast				135
Q3ZJ87 UniProt NPD GO	RK2_PSEAK	Chloroplast 50S ribosomal protein L2	0.41	-	mit	0	Plastid; chloroplast				278
Q85FJ9 UniProt NPD GO	RK20_ADICA	Chloroplast 50S ribosomal protein L20	0.41	-	nuc	0	Plastid; chloroplast				118
Q9MUP5 UniProt NPD GO	RK33_MESVI	Chloroplast 50S ribosomal protein L33	0.41	-	mit	0	Plastid; chloroplast				64
P62726 UniProt NPD GO	RK36_MAIZE	Chloroplast 50S ribosomal protein L36	0.41	-	mit	0	Plastid; chloroplast				37
Q6ENE0 UniProt NPD GO	RK36_ORYNI	Chloroplast 50S ribosomal protein L36	0.41	-	mit	0	Plastid; chloroplast				37
P62727 UniProt NPD GO	RK36_ORYSA	Chloroplast 50S ribosomal protein L36	0.41	-	mit	0	Plastid; chloroplast				37
Q6L368 UniProt NPD GO	RK36_SACHY	Chloroplast 50S ribosomal protein L36	0.41	-	mit	0	Plastid; chloroplast				37
Q6ENT0 UniProt NPD GO	RK36_SACOF	Chloroplast 50S ribosomal protein L36	0.41	-	mit	0	Plastid; chloroplast				37
P62728 UniProt NPD GO	RK36_WHEAT	Chloroplast 50S ribosomal protein L36	0.41	-	mit	0	Plastid; chloroplast				37
Q37050 UniProt NPD GO	CEMA_CHLRE	Chloroplast envelope membrane protein	0.41	-	mit	3	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				500
P06307 UniProt NPD GO	CCKN_HUMAN	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 58 (CCK58); Cholecystokinin 39 (CCK39); ...	0.41	-	exc	0			118440		115
Q03059 UniProt NPD GO	CLAT_MOUSE	Choline O-acetyltransferase (EC 2.3.1.6) (CHOACTase) (Choline acetylase) (ChAT)	0.41	-	nuc	0					640
Q6UVK1 UniProt NPD GO	CSPG4_HUMAN	Chondroitin sulfate proteoglycan 4 precursor (Chondroitin sulfate proteoglycan NG2) (Melanoma chondr ...	0.41	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Localized at the apical plasma m ...	cell surface [TAS]	601172		2322
P43609 UniProt NPD GO	RSC8_YEAST	Chromatin structure remodeling complex protein RSC8 (Remodel the structure of chromatin complex subu ...	0.41	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	nucleus [IDA] RSC complex [IDA]			557

You are viewing entries 30951 to 31000 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.