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
P19026 UniProt NPD GO	CDC21_PEA	Cell division control protein 2 homolog 1 (EC 2.7.11.22) (EC 2.7.11.23) (p34) (Fragment)	0.24	-	cyt	0					148
P00546 UniProt NPD GO	CDC28_YEAST	Cell division control protein 28 (EC 2.7.11.22)	0.24	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			298
Q06697 UniProt NPD GO	CDC73_YEAST	Cell division control protein 73 (RNA polymerase-associated protein CDC73)	0.24	-	nuc	0	Nucleus; nucleoplasm	Cdc73/Paf1 complex [IPI] nucleus [IDA]			393
Q9FH02 UniProt NPD GO	FTSH2_ARATH	Cell division protein ftsH homolog 2, chloroplast precursor (EC 3.4.24.-)	0.24	-	mit	0	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				704
Q10235 UniProt NPD GO	ALP11_SCHPO	Cell polarity protein alp11 (Altered polarity protein 11)	0.24	-	nuc	0	Cytoplasm	cytoplasm [IDA]			234
O48946 UniProt NPD GO	CESA1_ARATH	Cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (AtCesA-1) (Radially swollen pr ...	0.24	-	end	6	Cell membrane; multi-pass membrane protein (Probable)				1081
P48402 UniProt NPD GO	CHSB_IPOTF	Chalcone synthase B (EC 2.3.1.74) (Naringenin-chalcone synthase B) (CHS-B) (Fragment)	0.24	-	mit	0					366
Q9CQ10 UniProt NPD GO	CHMP3_MOUSE	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.24	-	nuc	0	Cytoplasm; cytosol. Membrane; lipid-anchor				223
Q8CGS4 UniProt NPD GO	CHMP3_RAT	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24) ...	0.24	-	nuc	0	Cytoplasm; cytosol. Membrane; lipid-anchor				222
P51794 UniProt NPD GO	CLCN4_RAT	Chloride channel protein 4 (ClC-4)	0.24	-	end	10	Membrane; multi-pass membrane protein				747
Q9Z1Q5 UniProt NPD GO	CLIC1_MOUSE	Chloride intracellular channel protein 1 (Nuclear chloride ion channel 27) (NCC27)	0.24	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	brush border [ISS] cytoplasm [ISS] membrane fraction [ISS] soluble fraction [ISS]			240
O00299 UniProt NPD GO	CLIC1_HUMAN	Chloride intracellular channel protein 1 (Nuclear chloride ion channel 27) (NCC27) (Chloride channel ...	0.24	-	cyt	0	Nucleus. Nucleus; nuclear membrane. Mostly in the nucleus including in the nuclear membrane. Cytopla ...	brush border [TAS] cytoplasm [IDA] membrane fraction [IDA] nuclear envelope [IDA] nucleus [TAS] soluble fraction [IDA]	602872	1RK4	240
Q5M883 UniProt NPD GO	CLIC2_RAT	Chloride intracellular channel protein 2	0.24	-	cyt	0					245
Q8BXK9 UniProt NPD GO	CLIC5_MOUSE	Chloride intracellular channel protein 5	0.24	-	cyt	0		actin cytoskeleton [ISS] insoluble fraction [ISS] microvillus [ISS]			251
Q32RU8 UniProt NPD GO	RR11_STAPU	Chloroplast 30S ribosomal protein S11	0.24	+	nuc	0	Plastid; chloroplast				130
Q9MDK3 UniProt NPD GO	RR12_OENHO	Chloroplast 30S ribosomal protein S12	0.24	-	mit	0	Plastid; chloroplast				123
Q9TLV0 UniProt NPD GO	RR13_CYACA	Chloroplast 30S ribosomal protein S13	0.24	-	mit	0	Plastid; chloroplast				122
P06374 UniProt NPD GO	RR16_TOBAC	Chloroplast 30S ribosomal protein S16	0.24	-	mit	0	Plastid; chloroplast				85
Q9MTI5 UniProt NPD GO	RR19_OENHO	Chloroplast 30S ribosomal protein S19	0.24	-	mit	0	Plastid; chloroplast				92
Q85CS9 UniProt NPD GO	RR3_ANTFO	Chloroplast 30S ribosomal protein S3	0.24	-	cyt	0	Plastid; chloroplast				218
Q332T8 UniProt NPD GO	RR3_LACSA	Chloroplast 30S ribosomal protein S3	0.24	-	cyt	0	Plastid; chloroplast				218
Q9BBP8 UniProt NPD GO	RR3_LOTJA	Chloroplast 30S ribosomal protein S3	0.24	-	mit	0	Plastid; chloroplast				218
Q6EW13 UniProt NPD GO	RR3_NYMAL	Chloroplast 30S ribosomal protein S3	0.24	-	mit	0	Plastid; chloroplast				218
Q6END5 UniProt NPD GO	RR3_ORYNI	Chloroplast 30S ribosomal protein S3	0.24	-	mit	0	Plastid; chloroplast				239
P12146 UniProt NPD GO	RR3_ORYSA	Chloroplast 30S ribosomal protein S3	0.24	-	mit	0	Plastid; chloroplast				239
P59033 UniProt NPD GO	RR8_PHAAN	Chloroplast 30S ribosomal protein S8	0.24	-	cyt	0	Plastid; chloroplast				134
Q6YXL1 UniProt NPD GO	RR8_PHYPA	Chloroplast 30S ribosomal protein S8	0.24	-	mit	0	Plastid; chloroplast				132
P05726 UniProt NPD GO	RK16_CHLRE	Chloroplast 50S ribosomal protein L16	0.24	-	mit	0	Plastid; chloroplast				136
P51307 UniProt NPD GO	RK16_PORPU	Chloroplast 50S ribosomal protein L16	0.24	-	nuc	0	Plastid; chloroplast				139
Q3V4Z4 UniProt NPD GO	RK22_ACOCL	Chloroplast 50S ribosomal protein L22	0.24	-	nuc	0	Plastid; chloroplast				127
Q9MTI6 UniProt NPD GO	RK22_OENHO	Chloroplast 50S ribosomal protein L22	0.24	-	nuc	0	Plastid; chloroplast				137
Q9TL23 UniProt NPD GO	RK5_NEPOL	Chloroplast 50S ribosomal protein L5	0.24	-	mit	0	Plastid; chloroplast				184
O95196 UniProt NPD GO	CSPG5_HUMAN	Chondroitin sulfate proteoglycan 5 precursor (Neuroglycan C) (Acidic leucine-rich EGF-like domain-co ...	0.24	-	exc	1	Cell membrane; single-pass type I membrane protein (By similarity). Endoplasmic reticulum; endoplasm ...	Golgi apparatus [IDA] Golgi-associated vesicle membrane [IDA] integral to plasma membrane [TAS] membrane fraction [TAS]	606775		566
Q9ERQ6 UniProt NPD GO	CSPG5_RAT	Chondroitin sulfate proteoglycan 5 precursor (Neuroglycan C) (Acidic leucine-rich EGF-like domain-co ...	0.24	-	exc	2 *	Cell membrane; single-pass type I membrane protein. Endoplasmic reticulum; endoplasmic reticulum mem ...				571
Q6FN68 UniProt NPD GO	EAF3_CANGA	Chromatin modification-related protein EAF3	0.24	-	cyt	0	Nucleus (By similarity)				355
P07852 UniProt NPD GO	ICE2_ASCSU	Chymotrypsin/elastase isoinhibitors 2 to 5	0.24	-	nuc	0	Secreted protein				65
P30516 UniProt NPD GO	1B01_SAGOE	Class I histocompatibility antigen, B alpha chain precursor	0.24	-	end	1	Membrane; single-pass type I membrane protein				365
Q8K3A0 UniProt NPD GO	HSC20_MOUSE	Co-chaperone protein HscB, mitochondrial precursor (Hsc20)	0.24	-	nuc	0	Mitochondrion (Potential)				234
Q58D49 UniProt NPD GO	MMAB_BOVIN	Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial precursor (EC 2.5.1.17) (Cob(I)alam ...	0.24	-	nuc	0	Mitochondrion (By similarity)				241
P82849 UniProt NPD GO	CBT2_NAJKA	Cobrotoxin II (CBT II) (Short neurotoxin 5) (Short neurotoxin 1)	0.24	-	nuc	0	Secreted protein			1G6M	62
P59275 UniProt NPD GO	NXSB_NAJKA	Cobrotoxin b (CBT b) (Short neurotoxin)	0.24	-	nuc	0	Secreted protein (By similarity)				61
Q9DE57 UniProt NPD GO	NXS2_NAJAT	Cobrotoxin homolog 2 precursor	0.24	-	nuc	0	Secreted protein				83
Q5E9F7 UniProt NPD GO	COF1_BOVIN	Cofilin-1 (Cofilin, non-muscle isoform)	0.24	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				165
Q4R5C0 UniProt NPD GO	COF1_MACFA	Cofilin-1 (Cofilin, non-muscle isoform)	0.24	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				165
P18760 UniProt NPD GO	COF1_MOUSE	Cofilin-1 (Cofilin, non-muscle isoform)	0.24	+	cyt	0	Nucleus. Cytoplasm. Almost completely in nucleus in cells exposed to heat shock or 10% dimethyl sulf ...	cortical actin cytoskeleton [IDA] cytoplasm [IDA]			165
P10668 UniProt NPD GO	COF1_PIG	Cofilin-1 (Cofilin, non-muscle isoform)	0.24	+	cyt	0	Nucleus. Cytoplasm. Almost completely in nucleus in cells exposed to heat shock or 10% dimethyl sulf ...				165
Q6B7M7 UniProt NPD GO	COF1_SHEEP	Cofilin-1 (Cofilin, non-muscle isoform)	0.24	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				165
Q923P0 UniProt NPD GO	COKA1_MOUSE	Collagen alpha-1(XX) chain (Fragment)	0.24	-	mit	0	Secreted protein; extracellular space (Probable)				765
Q9BXR6 UniProt NPD GO	FHR5_HUMAN	Complement factor H-related protein 5 precursor (FHR-5)	0.24	-	exc	0	Secreted protein	extracellular region [NAS]	608593		569
P69770 UniProt NPD GO	CX2_CONMR	Conotoxin Gla-MrII	0.24	-	nuc	0	Secreted protein				50

You are viewing entries 46151 to 46200 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.