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
O22932 UniProt NPD GO	CPK11_ARATH	CBL-interacting serine/threonine-protein kinase 11 (EC 2.7.11.1) (SOS2-like protein kinase PKS5) (SO ...	0.33	+	nuc	0					435
Q95MQ5 UniProt NPD GO	CD40L_PIG	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.33	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			261
P13749 UniProt NPD GO	1A04_PANTR	CHLA class I histocompatibility antigen, A-126 alpha chain precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein				365
P13751 UniProt NPD GO	1B02_PANTR	CHLA class I histocompatibility antigen, B-2 alpha chain precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein				362
Q6ZXC9 UniProt NPD GO	SIA8D_BOVIN	CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase (EC 2.4.99.-) (Alpha-2,8-sialyltransferase ...	0.33	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				359
Q63829 UniProt NPD GO	COMD3_MOUSE	COMM domain-containing protein 3 (Bmi-1 upstream gene protein) (Bup protein)	0.33	-	nuc	0					195
Q9P000 UniProt NPD GO	COMD9_HUMAN	COMM domain-containing protein 9	0.33	-	nuc	0					198
Q6CXL5 UniProt NPD GO	CSN10_KLULA	COP9 signalosome complex subunit 10	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				583
Q8W207 UniProt NPD GO	CSN2_ARATH	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (FUSCA protein 12) (FUSCA12)	0.33	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	nucleus [TAS]			439
Q6P4Z9 UniProt NPD GO	CSN8_RAT	COP9 signalosome complex subunit 8 (Signalosome subunit 8) (SGN8) (JAB1-containing signalosome subun ...	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				209
Q9Z0F4 UniProt NPD GO	KIP1_MOUSE	Calcium and integrin-binding protein 1 (Calmyrin) (DNA-PKcs-interacting protein) (Kinase-interacting ...	0.33	-	nuc	0	Membrane; lipid-anchor (By similarity)	cytoplasm [IMP] endoplasmic reticulum [ISS] membrane [IDA] nucleoplasm [ISS]			190
Q7TNJ7 UniProt NPD GO	KCC1G_RAT	Calcium/calmodulin-dependent protein kinase type 1G (EC 2.7.11.17) (CaM kinase IG) (CaM kinase I gam ...	0.33	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similari ...				476
Q3SYT6 UniProt NPD GO	CLGN_BOVIN	Calmegin precursor	0.33	+	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				606
O14967 UniProt NPD GO	CLGN_HUMAN	Calmegin precursor	0.33	+	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum [TAS]	601858		610
Q6FJ28 UniProt NPD GO	PALB_CANGA	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.33	-	cyt	0					713
P15253 UniProt NPD GO	CALR_RABIT	Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60)	0.33	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				418
Q9ER65 UniProt NPD GO	CSTN2_MOUSE	Calsyntenin-2 precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein (Potential)	postsynaptic membrane [IDA]			966
Q8VDA1 UniProt NPD GO	CSTN2_RAT	Calsyntenin-2 precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein (Potential)	postsynaptic membrane [IDA]			965
P04656 UniProt NPD GO	CAS1_CAVPO	Casein B precursor (Alpha-S1-casein)	0.33	-	exc	0	Secreted protein				198
P70343 UniProt NPD GO	CASP4_MOUSE	Caspase-4 precursor (EC 3.4.22.-) (CASP-4) (Caspase-11) (ICH-3 protease) [Contains: Caspase-4 subuni ...	0.33	-	cyt	0					373
Q32MD9 UniProt NPD GO	CDON_MOUSE	Cell adhesion molecule-related/down-regulated by oncogenes precursor	0.33	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				1250
O75004 UniProt NPD GO	CDC24_SCHPO	Cell division control protein 24	0.33	-	nuc	0	Nucleus (Potential)				501
O82150 UniProt NPD GO	FTSH_TOBAC	Cell division protein ftsH homolog, chloroplast precursor (EC 3.4.24.-) (DS9)	0.33	-	nuc	0	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				714
Q99795 UniProt NPD GO	GPA33_HUMAN	Cell surface A33 antigen precursor (Glycoprotein A33)	0.33	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602171		319
P20792 UniProt NPD GO	DAF1_CAEEL	Cell-surface receptor daf-1 precursor (EC 2.7.11.30) (Abnormal dauer formation protein 1)	0.33	-	end	1	Membrane; single-pass type I membrane protein				669
Q9SWW6 UniProt NPD GO	CESA7_ARATH	Cellulose synthase A catalytic subunit 7 [UDP-forming] (EC 2.4.1.12) (AtCesA-7) (Irregular xylem pro ...	0.33	-	end	6	Cell membrane; multi-pass membrane protein (Probable)			1WEO	1026
O44218 UniProt NPD GO	ZW10_DROPS	Centromere/kinetochore protein zw10 (Mitotic 15 protein)	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Kinetochore (By similarity). Excluded from the n ...				718
Q9ZS40 UniProt NPD GO	CHS2_DAUCA	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2) (DcCHS2)	0.33	-	cyt	0					397
Q6PHF0 UniProt NPD GO	CHM1A_BRARE	Charged multivesicular body protein 1a (Chromatin-modifying protein 1a) (CHMP1a)	0.33	-	nuc	0	Cytoplasm (By similarity)				198
Q6NY88 UniProt NPD GO	CHMP3_BRARE	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.33	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				220
Q5RDJ7 UniProt NPD GO	CLCN3_PONPY	Chloride channel protein 3 (ClC-3)	0.33	-	end	9	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein (By similarity). End ...				801
Q8RXR2 UniProt NPD GO	CLCF_ARATH	Chloride channel protein CLC-f (AtCLC-f)	0.33	-	end	8	Membrane; multi-pass membrane protein				781
Q5SD26 UniProt NPD GO	RR11_HUPLU	Chloroplast 30S ribosomal protein S11	0.33	-	mit	0	Plastid; chloroplast				132
Q85CF2 UniProt NPD GO	RR16_ANTFO	Chloroplast 30S ribosomal protein S16	0.33	-	mit	0	Plastid; chloroplast				84
P49503 UniProt NPD GO	RR16_ODOSI	Chloroplast 30S ribosomal protein S16	0.33	-	nuc	0	Plastid; chloroplast				79
Q85FV4 UniProt NPD GO	RR17_CYAME	Chloroplast 30S ribosomal protein S17	0.33	-	nuc	0	Plastid; chloroplast				82
Q85FR8 UniProt NPD GO	RR20_CYAME	Chloroplast 30S ribosomal protein S20	0.33	-	nuc	0	Plastid; chloroplast				74
P06586 UniProt NPD GO	RR3_MAIZE	Chloroplast 30S ribosomal protein S3	0.33	-	nuc	0	Plastid; chloroplast				224
Q6L3G0 UniProt NPD GO	RR3_SACHY	Chloroplast 30S ribosomal protein S3	0.33	-	nuc	0	Plastid; chloroplast				224
Q6ENS5 UniProt NPD GO	RR3_SACOF	Chloroplast 30S ribosomal protein S3	0.33	-	nuc	0	Plastid; chloroplast				224
P82129 UniProt NPD GO	RR7_SPIOL	Chloroplast 30S ribosomal protein S7	0.33	-	nuc	0	Plastid; chloroplast				154
P59775 UniProt NPD GO	RR8_CHLRE	Chloroplast 30S ribosomal protein S8	0.33	-	nuc	0	Plastid; chloroplast				141
O98458 UniProt NPD GO	RR8_SPIMX	Chloroplast 30S ribosomal protein S8	0.33	-	nuc	0	Plastid; chloroplast				132
Q85FI5 UniProt NPD GO	RK16_ADICA	Chloroplast 50S ribosomal protein L16	0.33	-	mit	0	Plastid; chloroplast				137
Q8M9V1 UniProt NPD GO	RK16_CHAGL	Chloroplast 50S ribosomal protein L16	0.33	-	mit	0	Plastid; chloroplast				138
O46901 UniProt NPD GO	RK16_GUITH	Chloroplast 50S ribosomal protein L16	0.33	-	mit	0	Plastid; chloroplast				134
P51270 UniProt NPD GO	RK35_PORPU	Chloroplast 50S ribosomal protein L35	0.33	-	mit	0	Plastid; chloroplast				65
Q9Z0E2 UniProt NPD GO	CHRD_MOUSE	Chordin precursor	0.33	-	exc	0	Secreted protein (By similarity)	extracellular space [IDA]			948
P16038 UniProt NPD GO	CSH_SHEEP	Chorionic somatomammotropin hormone precursor (Placental lactogen) (PL)	0.33	-	nuc	0	Secreted protein			1F6F	236
P93045 UniProt NPD GO	BSH_ARATH	Chromatin structure remodeling complex protein BSH (Protein bushy) (SNF5 homolog)	0.33	-	cyt	0	Nucleus				240

You are viewing entries 37401 to 37450 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.