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
O75493 UniProt NPD GO	CAH11_HUMAN	Carbonic anhydrase-related protein 2 precursor (CARP-2) (CA-RP II) (CA-XI) (Carbonic anhydrase-relat ...	0.40	-	exc	0	Secreted protein (Potential)		604644		328
P40229 UniProt NPD GO	CSK2C_ARATH	Casein kinase II subunit beta' (CK II beta')	0.40	-	nuc	0					282
Q53B88 UniProt NPD GO	CAR15_HYLLA	Caspase recruitment domain-containing protein 15	0.40	-	cyt	0	Cytoplasm (By similarity)				1040
P06115 UniProt NPD GO	CATT_YEAST	Catalase T (EC 1.11.1.6)	0.40	-	cyt	0	Cytoplasm	cytoplasm [TAS]			573
O35158 UniProt NPD GO	CDON_RAT	Cell adhesion molecule-related/down-regulated by oncogenes precursor	0.40	-	exc	1	Membrane; single-pass membrane protein (Potential)				1256
Q5R6C0 UniProt NPD GO	CC50A_PONPY	Cell cycle control protein 50A (Transmembrane protein 30A)	0.40	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				361
Q92368 UniProt NPD GO	RCD1_SCHPO	Cell differentiation protein rcd1	0.40	-	cyt	0					283
Q13042 UniProt NPD GO	CDC16_HUMAN	Cell division cycle protein 16 homolog (CDC16Hs) (Anaphase-promoting complex subunit 6) (APC6) (Cycl ...	0.40	+	cyt	0	Centrosome. Colocalizes with CDC27 to the centrosome at all stages of the cell cycle and to the mito ...	centrosome [IDA] spindle microtubule [IDA]	603461		620
P50613 UniProt NPD GO	CDK7_HUMAN	Cell division protein kinase 7 (EC 2.7.11.22) (EC 2.7.11.23) (CDK-activating kinase) (CAK) (TFIIH ba ...	0.40	-	mit	0	Nucleus	nucleus [TAS]	601955	1UA2	346
Q9UUL4 UniProt NPD GO	MOK12_SCHPO	Cell wall alpha-1,3-glucan synthase mok12 (EC 2.4.1.183)	0.40	-	end	14 *					2352
O75689 UniProt NPD GO	CENA1_HUMAN	Centaurin-alpha 1 (Putative MAPK-activating protein PM25)	0.40	-	mit	0	Nucleus. Cytoplasm. Recruited to the plasma membrane upon epidermal growth factor-dependent activati ...	cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]	608114		374
Q7T339 UniProt NPD GO	CHMP5_BRARE	Charged multivesicular body protein 5 (Chromatin-modifying protein 5)	0.40	-	nuc	0	Cytoplasm (By similarity)				220
Q9N2G5 UniProt NPD GO	CLIC6_RABIT	Chloride intracellular channel 6 (Parchorin)	0.40	-	nuc	0	Cytoplasm. Predominantly. Cell membrane. Upon chloride ion efflux from the cell, it is translocated ...				637
Q9MUU9 UniProt NPD GO	RR11_MESVI	Chloroplast 30S ribosomal protein S11	0.40	-	mit	0	Plastid; chloroplast				130
P56354 UniProt NPD GO	RR12_CHLVU	Chloroplast 30S ribosomal protein S12	0.40	-	mit	0	Plastid; chloroplast				123
Q85X49 UniProt NPD GO	RR12_PINKO	Chloroplast 30S ribosomal protein S12	0.40	-	nuc	0	Plastid; chloroplast				123
Q85FI2 UniProt NPD GO	RR19_ADICA	Chloroplast 30S ribosomal protein S19	0.40	-	mit	0	Plastid; chloroplast				92
P56799 UniProt NPD GO	RR4_ARATH	Chloroplast 30S ribosomal protein S4	0.40	-	mit	0	Plastid; chloroplast				201
Q4G3A4 UniProt NPD GO	RR4_EMIHU	Chloroplast 30S ribosomal protein S4	0.40	-	mit	0	Plastid; chloroplast				202
P06358 UniProt NPD GO	RR4_MARPO	Chloroplast 30S ribosomal protein S4	0.40	-	mit	0	Plastid; chloroplast				202
Q9M4C2 UniProt NPD GO	RR4_RICNA	Chloroplast 30S ribosomal protein S4	0.40	-	mit	0	Plastid; chloroplast				202
P59150 UniProt NPD GO	RR4_TAKLE	Chloroplast 30S ribosomal protein S4	0.40	-	mit	0	Plastid; chloroplast				202
Q9GFK8 UniProt NPD GO	RR7_LACFR	Chloroplast 30S ribosomal protein S7	0.40	-	nuc	0	Plastid; chloroplast				155
Q9BBP9 UniProt NPD GO	RK16_LOTJA	Chloroplast 50S ribosomal protein L16	0.40	-	mit	0	Plastid; chloroplast				135
P06383 UniProt NPD GO	RK16_MARPO	Chloroplast 50S ribosomal protein L16	0.40	-	mit	0	Plastid; chloroplast				143
Q6EW14 UniProt NPD GO	RK16_NYMAL	Chloroplast 50S ribosomal protein L16	0.40	-	mit	0	Plastid; chloroplast				135
P12138 UniProt NPD GO	RK16_ORYSA	Chloroplast 50S ribosomal protein L16	0.40	-	mit	0	Plastid; chloroplast				136
P60407 UniProt NPD GO	RK2_PHYPA	Chloroplast 50S ribosomal protein L2	0.40	-	nuc	0	Plastid; chloroplast				277
Q9MUT8 UniProt NPD GO	RK23_MESVI	Chloroplast 50S ribosomal protein L23	0.40	-	nuc	0	Plastid; chloroplast				92
Q8M9U3 UniProt NPD GO	RK32_CHAGL	Chloroplast 50S ribosomal protein L32	0.40	-	nuc	0	Plastid; chloroplast				57
Q9MTJ1 UniProt NPD GO	RK36_OENHO	Chloroplast 50S ribosomal protein L36	0.40	-	mit	0	Plastid; chloroplast				37
P50144 UniProt NPD GO	CCKN1_XENLA	Cholecystokinin type 1 precursor [Contains: Cholecystokinin (CCK)]	0.40	-	exc	0					123
Q9P2E5 UniProt NPD GO	CHGUT_HUMAN	Chondroitin sulfate glucuronyltransferase (EC 2.4.1.226) (N-acetylgalactosaminyl-proteoglycan 3-beta ...	0.40	-	end	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)		608037		772
Q8VHY0 UniProt NPD GO	CSPG4_MOUSE	Chondroitin sulfate proteoglycan 4 precursor (Chondroitin sulfate proteoglycan NG2) (AN2 proteoglyca ...	0.40	-	end	1	Cell membrane; single-pass type I membrane protein. Localized at the apical plasma membrane it reloc ...	plasma membrane [IDA]			2327
P58239 UniProt NPD GO	LECT1_BRARE	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) [Contain ...	0.40	-	mit	1 *	Cytoplasm (By similarity). Secreted protein (By similarity). Accumulated in the inter-territorial ma ...				286
P39995 UniProt NPD GO	EAF5_YEAST	Chromatin modification-related protein EAF5 (ESA1-associated factor 5)	0.40	-	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI] nucleus [IDA]			279
P53675 UniProt NPD GO	CLH2_HUMAN	Clathrin heavy chain 2 (CLH-22)	0.40	-	nuc	0	Cytoplasmic face of coated pits and vesicles (By similarity)		601273		1640
P32798 UniProt NPD GO	COT1_YEAST	Cobalt uptake protein COT1	0.40	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein. Another possibility exists that ...	mitochondrion [IDA] vacuole (sensu Fungi) [IDA]			439
P60771 UniProt NPD GO	NXS1_NAJKA	Cobrotoxin (CBT)	0.40	-	nuc	0	Secreted protein				62
Q78PG9 UniProt NPD GO	CCD25_MOUSE	Coiled-coil domain-containing protein 25	0.40	+	nuc	0					208
Q5R9S1 UniProt NPD GO	CCD25_PONPY	Coiled-coil domain-containing protein 25	0.40	+	nuc	0					208
P26154 UniProt NPD GO	CR14_HORVU	Cold-regulated protein BLT14	0.40	-	nuc	0					88
Q60847 UniProt NPD GO	COCA1_MOUSE	Collagen alpha-1(XII) chain precursor	0.40	-	cyt	0					3119
P53079 UniProt NPD GO	COG1_YEAST	Conserved oligomeric Golgi complex subunit 1 (COG complex subunit 1) (Complexed with DOR1 protein 3) ...	0.40	-	nuc	0		Golgi transport complex [IPI]			417
P53271 UniProt NPD GO	COG2_YEAST	Conserved oligomeric Golgi complex subunit 2 (COG complex subunit 2) (Protein SEC35)	0.40	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side	Golgi transport complex [IPI] peripheral to membrane of membrane fraction [IDA] soluble fraction [IDA]			262
Q9QZQ8 UniProt NPD GO	H2AY_MOUSE	Core histone macro-H2A.1 (Histone macroH2A1) (mH2A1) (H2A.y) (H2A/y)	0.40	+	mit	0	Nucleus. Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin. I ...	centrosome [TAS] condensed chromosome [IDA] nucleus [IDA]			371
P80223 UniProt NPD GO	DEF7_RABIT	Corticostatin-6 (Corticostatin VI) (CS-VI) (Neutrophil antibiotic peptide NP-6)	0.40	-	mit	0	Secreted protein				34
P33524 UniProt NPD GO	CRU2_BRANA	Cruciferin BnC2 precursor (11S globulin) (12S storage protein) [Contains: Cruciferin BnC2 subunit al ...	0.40	-	exc	0					496
P97766 UniProt NPD GO	CFC1_MOUSE	Cryptic protein precursor	0.40	-	nuc	0					202
Q92772 UniProt NPD GO	CDKL2_HUMAN	Cyclin-dependent kinase-like 2 (EC 2.7.11.22) (Serine/threonine-protein kinase KKIAMRE) (Protein kin ...	0.40	-	cyt	0	Cytoplasm. Nucleus		603442		493

You are viewing entries 31701 to 31750 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.