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
P42158 UniProt NPD GO	KC1D_ARATH	Casein kinase I isoform delta-like (EC 2.7.11.1) (CKI-delta)	0.55	-	nuc	0	Cytoplasm (By similarity)				450
Q60649 UniProt NPD GO	CLPB_MOUSE	Caseinolytic peptidase B protein homolog (Suppressor of potassium transport defect 3)	0.55	-	mit	0					677
Q9WTT2 UniProt NPD GO	CLPB_RAT	Caseinolytic peptidase B protein homolog (Suppressor of potassium transport defect 3)	0.55	-	mit	0					677
P29594 UniProt NPD GO	CASP2_MOUSE	Caspase-2 precursor (EC 3.4.22.-) (CASP-2) (ICH-1 protease) (NEDD2 protein) (Neural precursor cell e ...	0.55	-	nuc	0		nucleus [IDA]			452
Q8IRY7 UniProt NPD GO	CASP8_DROME	Caspase-8 precursor (EC 3.4.22.-) (Death-related Ced-3/NEDD2-like protein) [Contains: Caspase-8 subu ...	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA]			516
Q07113 UniProt NPD GO	MPRI_MOUSE	Cation-independent mannose-6-phosphate receptor precursor (CI Man-6-P receptor) (CI-MPR) (M6PR) (Ins ...	0.55	-	end	1	Lysosome; lysosomal membrane; single-pass type I membrane protein	nuclear envelope lumen [IDA] nucleus [IDA]			2483
Q60Z52 UniProt NPD GO	CED4_CAEBR	Cell death protein 4	0.55	-	cyt	0	Mitochondrion (By similarity). In non cell death induced cells. Ced-9 is required for mitochondrial ...				554
P50750 UniProt NPD GO	CDK9_HUMAN	Cell division protein kinase 9 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9) (Serine/thr ...	0.55	-	nuc	0	Nucleus	nucleus [TAS] transcription elongation factor complex [TAS]	603251	1PF6	372
Q29480 UniProt NPD GO	P53_EQUAS	Cellular tumor antigen p53 (Tumor suppressor p53) (Fragment)	0.55	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				207
Q9Y738 UniProt NPD GO	MIS12_SCHPO	Centromere protein mis12	0.55	+	cyt	0	Nucleus. Centromeric	inner kinetochore of condensed chromosome [TAS]			259
Q9FYB5 UniProt NPD GO	DNJ11_ARATH	Chaperone protein dnaJ 11, chloroplast precursor (AtJ11) (AtDjC11)	0.55	-	mit	0	Plastid; chloroplast; chloroplast stroma. Probably also in other plastids				161
Q92444 UniProt NPD GO	CHS2_PARBR	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-II chitin synt ...	0.55	-	end	7	Cell membrane; multi-pass membrane protein				1043
Q9MUP6 UniProt NPD GO	RR18_MESVI	Chloroplast 30S ribosomal protein S18	0.55	-	nuc	0	Plastid; chloroplast				71
P51253 UniProt NPD GO	RR20_PORPU	Chloroplast 30S ribosomal protein S20	0.55	-	nuc	0	Plastid; chloroplast				94
Q6H9K8 UniProt NPD GO	RR4_EQUPA	Chloroplast 30S ribosomal protein S4	0.55	-	nuc	0	Plastid; chloroplast				207
Q6ENH2 UniProt NPD GO	RR4_ORYNI	Chloroplast 30S ribosomal protein S4	0.55	-	mit	0	Plastid; chloroplast				201
P12147 UniProt NPD GO	RR4_ORYSA	Chloroplast 30S ribosomal protein S4	0.55	-	mit	0	Plastid; chloroplast				201
P41638 UniProt NPD GO	RR4_PINTH	Chloroplast 30S ribosomal protein S4	0.55	-	mit	0	Plastid; chloroplast				198
O20219 UniProt NPD GO	RR4_GLAMU	Chloroplast 30S ribosomal protein S4 (Fragment)	0.55	-	mit	0	Plastid; chloroplast				195
O20221 UniProt NPD GO	RR4_GLAPA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.55	-	mit	0	Plastid; chloroplast				197
O20255 UniProt NPD GO	RR4_LAPNE	Chloroplast 30S ribosomal protein S4 (Fragment)	0.55	-	mit	0	Plastid; chloroplast				183
P36465 UniProt NPD GO	RR4_MELAL	Chloroplast 30S ribosomal protein S4 (Fragment)	0.55	-	mit	0	Plastid; chloroplast				196
O20278 UniProt NPD GO	RR4_PILTE	Chloroplast 30S ribosomal protein S4 (Fragment)	0.55	-	mit	0	Plastid; chloroplast				195
Q71L16 UniProt NPD GO	RR7_CEDDE	Chloroplast 30S ribosomal protein S7	0.55	-	nuc	0	Plastid; chloroplast				155
Q8S8V8 UniProt NPD GO	RR8_ATRBE	Chloroplast 30S ribosomal protein S8	0.55	-	nuc	0	Plastid; chloroplast				134
Q68RX1 UniProt NPD GO	RR8_PANGI	Chloroplast 30S ribosomal protein S8	0.55	-	nuc	0	Plastid; chloroplast				134
Q3V4X1 UniProt NPD GO	RK2_ACOCL	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				273
Q85B65 UniProt NPD GO	RK2_ANTFO	Chloroplast 50S ribosomal protein L2	0.55	-	nuc	0	Plastid; chloroplast				277
P56791 UniProt NPD GO	RK2_ARATH	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q9B1H9 UniProt NPD GO	RK2_LOTJA	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q2MI59 UniProt NPD GO	RK2_LYCES	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q3C1N6 UniProt NPD GO	RK2_NICSY	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q33BZ0 UniProt NPD GO	RK2_NICTO	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q68RU2 UniProt NPD GO	RK2_PANGI	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q2MIE6 UniProt NPD GO	RK2_SOLBU	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q2VEB7 UniProt NPD GO	RK2_SOLTU	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
P06379 UniProt NPD GO	RK2_TOBAC	Chloroplast 50S ribosomal protein L2	0.55	+	nuc	0	Plastid; chloroplast				274
Q8S8V3 UniProt NPD GO	RK2A_ATRBE	Chloroplast 50S ribosomal protein L2-1	0.55	+	nuc	0	Plastid; chloroplast				274
Q7YJT9 UniProt NPD GO	RK22_CALFE	Chloroplast 50S ribosomal protein L22	0.55	-	mit	0	Plastid; chloroplast				140
Q95H48 UniProt NPD GO	RK22_WHEAT	Chloroplast 50S ribosomal protein L22	0.55	-	nuc	0	Plastid; chloroplast				148
Q5D0K2 UniProt NPD GO	CCKAR_CANFA	Cholecystokinin type A receptor (CCK-A receptor) (CCK-AR) (Cholecystokinin-1 receptor) (CCK1-R)	0.55	+	end	7 *	Membrane; multi-pass membrane protein				428
O54783 UniProt NPD GO	CHKB_RAT	Choline/ethanolamine kinase [Includes: Choline kinase beta (EC 2.7.1.32) (CK); Ethanolamine kinase ( ...	0.55	-	cyt	0					393
Q86X52 UniProt NPD GO	CHSS1_HUMAN	Chondroitin sulfate synthase 1 (EC 2.4.1.175) (Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-be ...	0.55	-	vac	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)		608183		802
Q01522 UniProt NPD GO	CF23_DROME	Chorion transcription factor Cf2, isoform III	0.55	-	nuc	0	Nucleus	nucleus [IDA]			514
Q61686 UniProt NPD GO	CBX5_MOUSE	Chromobox protein homolog 5 (Heterochromatin protein 1 homolog alpha) (HP1 alpha)	0.55	+	nuc	0	Nucleus. Component of centromeric and pericentromeric heterochromatin. Associates with chromosomes d ...	kinetochore [IDA] nuclear heterochromatin [IDA]			191
P23093 UniProt NPD GO	CSP_PLABA	Circumsporozoite protein precursor (CS)	0.55	-	exc	1 *					347
Q16630 UniProt NPD GO	CPSF6_HUMAN	Cleavage and polyadenylation specificity factor 6 (Cleavage and polyadenylation specificity factor 6 ...	0.55	+	nuc	0	Nucleus. In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckl ...	nucleus [TAS]	604979		551
Q6DEL2 UniProt NPD GO	CLPT1_BRARE	Cleft lip and palate transmembrane protein 1 homolog	0.55	-	end	5	Membrane; multi-pass membrane protein (Potential)				631
Q6AZI2 UniProt NPD GO	CCD47_XENLA	Coiled-coil domain-containing protein 47 precursor	0.55	-	end	0	Membrane; single-pass membrane protein (Potential)				489
Q9BUK0 UniProt NPD GO	CHCH7_HUMAN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 7	0.55	-	nuc	0					85

You are viewing entries 21851 to 21900 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.