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
P32893 UniProt NPD GO	KRE11_YEAST	Beta-glucan synthesis-associated protein KRE11 (Killer toxin-resistance protein 11)	0.52	-	nuc	0	Cytoplasm	TRAPP complex [IDA]			560
P06300 UniProt NPD GO	PDYN_RAT	Beta-neoendorphin-dynorphin precursor (Proenkephalin B) (Preprodynorphin) [Contains: Alpha-neoendorp ...	0.52	-	exc	0	Secreted protein				248
P01214 UniProt NPD GO	PDYN_PIG	Beta-neoendorphin-dynorphin precursor (Proenkephalin B) (Preprodynorphin) [Contains: Beta-neoendorph ...	0.52	-	exc	0	Secreted protein				256
P05200 UniProt NPD GO	NGF_CHICK	Beta-nerve growth factor precursor (Beta-NGF)	0.52	-	exc	0	Secreted protein				243
Q7TNI2 UniProt NPD GO	BSMAP_MOUSE	Brain-specific membrane-anchored protein precursor	0.52	-	exc	1	Membrane (Potential). Could be associated with an intracellular organelle or membrane (Potential)				337
Q08004 UniProt NPD GO	BUD20_YEAST	Bud site selection protein 20	0.52	-	nuc	0	Nucleus. Endoplasmic reticulum	nucleus [IDA]			166
P23950 UniProt NPD GO	TISB_MOUSE	Butyrate response factor 1 (TIS11B protein)	0.52	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			338
P17431 UniProt NPD GO	TISB_RAT	Butyrate response factor 1 (TIS11B protein) (EGF-inducible protein CMG1)	0.52	-	nuc	0	Nucleus	cytosol [IDA]			338
P41156 UniProt NPD GO	ETS1_RAT	C-ets-1 protein (p54)	0.52	+	nuc	0	Nucleus	nucleus [ISS]			441
Q8K199 UniProt NPD GO	CP061_MOUSE	C16orf61 protein homolog	0.52	-	nuc	0					79
Q6FIP7 UniProt NPD GO	CSN11_CANGA	COP9 signalosome complex subunit 11	0.52	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				452
P15116 UniProt NPD GO	CADH2_MOUSE	Cadherin-2 precursor (Neural-cadherin) (N-cadherin) (CDw325 antigen)	0.52	-	end	1	Membrane; single-pass type I membrane protein	adherens junction [IDA] lamellipodium [IDA] synapse [IDA]		1OP4	906
O18866 UniProt NPD GO	KCMA1_PIG	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.52	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1152
Q9BG98 UniProt NPD GO	KCMA1_RABIT	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.52	-	end	6	Membrane; multi-pass membrane protein. Isoform 4: Endoplasmic reticulum; endoplasmic reticulum membr ...				1179
Q24956 UniProt NPD GO	CATR_GIALA	Caltractin (Centrin)	0.52	-	mit	0	Centrosome. Centrosome of interphase and mitotic cells				176
Q28689 UniProt NPD GO	MRP2_RABIT	Canalicular multispecific organic anion transporter 1 (ATP-binding cassette sub-family C member 2) ( ...	0.52	+	end	14 *	Membrane; multi-pass membrane protein (By similarity)				1564
P18334 UniProt NPD GO	CSK2A_CAEEL	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II subunit alpha)	0.52	-	cyt	0					360
Q9D9K3 UniProt NPD GO	AVEN_MOUSE	Cell death regulator Aven	0.52	-	nuc	0	Membrane; peripheral membrane protein. Associated with intracellular membranes (By similarity)	intracellular [ISS] membrane fraction [ISS]			342
P07834 UniProt NPD GO	CDC4_YEAST	Cell division control protein 4 (F-box protein CDC4) (E3 ubiquitin ligase complex SCF subunit CDC4)	0.52	-	nuc	0	Nucleus	nuclear SCF ubiquitin ligase complex [IDA]		1NEX	779
Q503V0 UniProt NPD GO	CHMP6_BRARE	Charged multivesicular body protein 6 (Chromatin-modifying protein 6)	0.52	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				205
Q1XDK2 UniProt NPD GO	RR10_PORYE	Chloroplast 30S ribosomal protein S10	0.52	-	nuc	0	Plastid; chloroplast				105
P02368 UniProt NPD GO	RR12_EUGGR	Chloroplast 30S ribosomal protein S12	0.52	-	nuc	0	Plastid; chloroplast				124
P08241 UniProt NPD GO	RR2_PEA	Chloroplast 30S ribosomal protein S2	0.52	-	cyt	0	Plastid; chloroplast				236
Q70Y01 UniProt NPD GO	RR4_AMBTC	Chloroplast 30S ribosomal protein S4	0.52	-	mit	0	Plastid; chloroplast				201
Q2L908 UniProt NPD GO	RR4_GOSHI	Chloroplast 30S ribosomal protein S4	0.52	-	mit	0	Plastid; chloroplast				201
P59146 UniProt NPD GO	RR4_LEUSC	Chloroplast 30S ribosomal protein S4	0.52	-	mit	0	Plastid; chloroplast				202
Q9BBT5 UniProt NPD GO	RR4_LOTJA	Chloroplast 30S ribosomal protein S4	0.52	-	mit	0	Plastid; chloroplast				201
P59149 UniProt NPD GO	RR4_NECCR	Chloroplast 30S ribosomal protein S4	0.52	-	mit	0	Plastid; chloroplast				202
Q95H61 UniProt NPD GO	RR4_WHEAT	Chloroplast 30S ribosomal protein S4	0.52	-	mit	0	Plastid; chloroplast				201
O19995 UniProt NPD GO	RR4_BABST	Chloroplast 30S ribosomal protein S4 (Fragment)	0.52	-	nuc	0	Plastid; chloroplast				183
O20236 UniProt NPD GO	RR4_ISOTA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.52	-	mit	0	Plastid; chloroplast				182
P36470 UniProt NPD GO	RR4_RHAHU	Chloroplast 30S ribosomal protein S4 (Fragment)	0.52	-	mit	0	Plastid; chloroplast				196
Q85AI6 UniProt NPD GO	RR7_ADICA	Chloroplast 30S ribosomal protein S7	0.52	-	nuc	0	Plastid; chloroplast				150
Q85B41 UniProt NPD GO	RR7_ANTFO	Chloroplast 30S ribosomal protein S7	0.52	-	nuc	0	Plastid; chloroplast				155
Q6KGW7 UniProt NPD GO	RR7_SAGLA	Chloroplast 30S ribosomal protein S7	0.52	-	mit	0	Plastid; chloroplast				155
P08530 UniProt NPD GO	RR8_MAIZE	Chloroplast 30S ribosomal protein S8	0.52	-	cyt	0	Plastid; chloroplast				136
Q6ENS8 UniProt NPD GO	RR8_SACOF	Chloroplast 30S ribosomal protein S8	0.52	-	cyt	0	Plastid; chloroplast				136
Q95H52 UniProt NPD GO	RR8_WHEAT	Chloroplast 30S ribosomal protein S8	0.52	-	cyt	0	Plastid; chloroplast				136
Q9TL29 UniProt NPD GO	RR9_NEPOL	Chloroplast 30S ribosomal protein S9	0.52	-	nuc	0	Plastid; chloroplast				134
P41651 UniProt NPD GO	RK32_PINTH	Chloroplast 50S ribosomal protein L32	0.52	-	nuc	0	Plastid; chloroplast				69
Q8M9X3 UniProt NPD GO	CEMA_CHAGL	Chloroplast envelope membrane protein	0.52	-	end	3	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				472
P49585 UniProt NPD GO	PCY1A_HUMAN	Choline-phosphate cytidylyltransferase A (EC 2.7.7.15) (Phosphorylcholine transferase A) (CTP:phosph ...	0.52	+	nuc	0	Cytoplasm; cytosol (By similarity). Membrane; peripheral membrane protein (By similarity). It can in ...	soluble fraction [TAS]	123695		367
P10645 UniProt NPD GO	CMGA_HUMAN	Chromogranin A precursor (CgA) (Pituitary secretory protein I) (SP-I) [Contains: Vasostatin-1 (Vasos ...	0.52	-	exc	0	Neuroendocrine and endocrine secretory granules		118910	1LV4	457
Q68FD5 UniProt NPD GO	CLH_MOUSE	Clathrin heavy chain	0.52	-	cyt	0	Cytoplasmic face of coated pits and vesicles (By similarity)	membrane coat [IDA] mitochondrion [IDA]			1675
P04975 UniProt NPD GO	CLCB_BOVIN	Clathrin light chain B (Lcb)	0.52	-	nuc	0	Cytoplasmic face of coated pits and vesicles				228
P09497 UniProt NPD GO	CLCB_HUMAN	Clathrin light chain B (Lcb)	0.52	-	nuc	0	Cytoplasmic face of coated pits and vesicles	clathrin coat [NAS]	118970		229
P00742 UniProt NPD GO	FA10_HUMAN	Coagulation factor X precursor (EC 3.4.21.6) (Stuart factor) (Stuart-Prower factor) [Contains: Facto ...	0.52	-	exc	1 *		extracellular region [NAS]	227600	2GD4	488
Q5SV66 UniProt NPD GO	CCD42_MOUSE	Coiled-coil domain-containing protein 42	0.52	-	nuc	0					312
Q8SPI2 UniProt NPD GO	CHCH7_MACFA	Coiled-coil-helix-coiled-coil-helix domain-containing protein 7	0.52	-	nuc	0					85
Q60467 UniProt NPD GO	CO5A1_CRILO	Collagen alpha-1(V) chain precursor	0.52	-	exc	1 *					1840

You are viewing entries 23601 to 23650 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.