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
Q90686 UniProt NPD GO	CATK_CHICK	Cathepsin K precursor (EC 3.4.22.38) (JTAP-1)	0.23	-	end	0					334
P40793 UniProt NPD GO	CDC42_DROME	Cdc42 homolog	0.23	-	cyt	0	Cell membrane; cell-cell junction; adherens junction; lipid-anchor. Adherens junctions of developing ...	adherens junction [IDA]			191
P60952 UniProt NPD GO	CDC42_CANFA	Cell division control protein 42 homolog precursor (G25K GTP-binding protein)	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
P60953 UniProt NPD GO	CDC42_HUMAN	Cell division control protein 42 homolog precursor (G25K GTP-binding protein)	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [IDA] filopodium [IDA] plasma membrane [IDA]	116952	2NGR	191
P60766 UniProt NPD GO	CDC42_MOUSE	Cell division control protein 42 homolog precursor (G25K GTP-binding protein)	0.23	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
Q99675 UniProt NPD GO	CGRF1_HUMAN	Cell growth regulator with RING finger domain 1 (Cell growth regulatory gene 19 protein)	0.23	-	mit	1 *			606138		332
Q9EPF2 UniProt NPD GO	MUC18_RAT	Cell surface glycoprotein MUC18 precursor (Melanoma-associated antigen MUC18) (Melanoma cell adhesio ...	0.23	-	exc	1	Cell membrane; single-pass type I membrane protein. Detected at the surface of the cell body of moto ...				648
Q07988 UniProt NPD GO	YL040_YEAST	Cell wall protein YLR040C precursor	0.23	-	exc	0	Cell wall; lipid-anchor; GPI-anchor. GPI-anchored cell wall protein (GPI-CWP)	cell wall (sensu Fungi) [IDA]			224
Q9CQS9 UniProt NPD GO	CEP27_MOUSE	Centrosomal protein of 27 kDa (Cep27 protein)	0.23	-	mit	0	Centrosome (By similarity)				234
P53415 UniProt NPD GO	CHS2_SECCE	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.23	-	cyt	0					394
O23731 UniProt NPD GO	CHS8_BROFI	Chalcone synthase 8 (EC 2.3.1.74) (Naringenin-chalcone synthase 8)	0.23	-	cyt	0					394
P29215 UniProt NPD GO	DNAK_GUITH	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.23	-	cyt	0	Plastid; chloroplast				627
Q921W0 UniProt NPD GO	CHM1A_MOUSE	Charged multivesicular body protein 1a (Chromatin-modifying protein 1a) (CHMP1a)	0.23	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein. Nucleus; nucleoplasm; nuclear ...	condensed nuclear chromosome [ISS] early endosome [ISS] endomembrane system [ISS] microtubule organizing center [ISS] nuclear matrix [ISS]			196
Q5R605 UniProt NPD GO	CHM1A_PONPY	Charged multivesicular body protein 1a (Chromatin-modifying protein 1a) (CHMP1a)	0.23	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				196
Q9HD42 UniProt NPD GO	CHM1A_HUMAN	Charged multivesicular body protein 1a (Chromatin-modifying protein 1a) (CHMP1a) (Vacuolar protein s ...	0.23	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein. Nucleus; nucleoplasm; nuclear ...	condensed nuclear chromosome [IDA] early endosome [IDA] endomembrane system [IDA] microtubule organizing center [IDA] nuclear matrix [IDA]	164010		196
P29070 UniProt NPD GO	CHS1_NEUCR	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-III chitin syn ...	0.23	-	end	7	Cell membrane; multi-pass membrane protein				917
Q9S8M0 UniProt NPD GO	LECT_SOLTU	Chitin-binding lectin 1 precursor (PL-I)	0.23	-	exc	0					323
P51793 UniProt NPD GO	CLCN4_HUMAN	Chloride channel protein 4 (ClC-4)	0.23	-	end	11	Membrane; multi-pass membrane protein		302910		760
Q61418 UniProt NPD GO	CLCN4_MOUSE	Chloride channel protein 4 (ClC-4)	0.23	-	end	10	Membrane; multi-pass membrane protein				747
Q29238 UniProt NPD GO	CLIC1_PIG	Chloride intracellular channel protein 1 (Nuclear chloride ion channel 27) (Fragment)	0.23	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				109
Q4G341 UniProt NPD GO	RR10_EMIHU	Chloroplast 30S ribosomal protein S10	0.23	-	cyt	0	Plastid; chloroplast				103
P07134 UniProt NPD GO	RR12_SOYBN	Chloroplast 30S ribosomal protein S12	0.23	-	mit	0	Plastid; chloroplast				123
Q9M3I4 UniProt NPD GO	RR15_SPIOL	Chloroplast 30S ribosomal protein S15	0.23	-	nuc	0	Plastid; chloroplast				90
Q5SCW6 UniProt NPD GO	RR16_HUPLU	Chloroplast 30S ribosomal protein S16	0.23	-	mit	0	Plastid; chloroplast				84
Q9TM33 UniProt NPD GO	RR2_CYACA	Chloroplast 30S ribosomal protein S2	0.23	-	nuc	0	Plastid; chloroplast				243
Q7YJU0 UniProt NPD GO	RR3_CALFE	Chloroplast 30S ribosomal protein S3	0.23	-	mit	0	Plastid; chloroplast				218
Q68RW8 UniProt NPD GO	RR3_PANGI	Chloroplast 30S ribosomal protein S3	0.23	-	mit	0	Plastid; chloroplast				219
P49544 UniProt NPD GO	RK1_ODOSI	Chloroplast 50S ribosomal protein L1	0.23	-	nuc	0	Plastid; chloroplast				230
P49551 UniProt NPD GO	RK13_ODOSI	Chloroplast 50S ribosomal protein L13	0.23	-	nuc	0	Plastid; chloroplast				139
Q9MUU3 UniProt NPD GO	RK16_MESVI	Chloroplast 50S ribosomal protein L16	0.23	-	mit	0	Plastid; chloroplast				136
Q85FW0 UniProt NPD GO	RK2_CYAME	Chloroplast 50S ribosomal protein L2	0.23	-	mit	0	Plastid; chloroplast				245
P51207 UniProt NPD GO	RK32_PORPU	Chloroplast 50S ribosomal protein L32	0.23	-	nuc	0	Plastid; chloroplast				59
P28528 UniProt NPD GO	RK36_GUITH	Chloroplast 50S ribosomal protein L36	0.23	-	nuc	0	Plastid; chloroplast				48
Q9MUU8 UniProt NPD GO	RK36_MESVI	Chloroplast 50S ribosomal protein L36	0.23	+	mit	0	Plastid; chloroplast				38
P01355 UniProt NPD GO	CCKN_RAT	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 39 (CCK39); Cholecystokinin 33 (CCK33); ...	0.23	-	exc	1 *	Secreted protein	extracellular region [NAS]			115
P09611 UniProt NPD GO	CSH1_BOVIN	Chorionic somatomammotropin hormone 1 precursor (Placental lactogen I) (BPLP-I)	0.23	-	nuc	0	Secreted protein				236
P05691 UniProt NPD GO	CSP_PLAFL	Circumsporozoite protein (CS) (Fragment)	0.23	-	nuc	0					315
P08675 UniProt NPD GO	CSP_PLACL	Circumsporozoite protein precursor (CS)	0.23	-	nuc	1					378
P13814 UniProt NPD GO	CSP_PLAFT	Circumsporozoite protein precursor (CS)	0.23	-	mit	0					424
P30517 UniProt NPD GO	1C01_SAGOE	Class I histocompatibility antigen, C alpha chain precursor	0.23	-	end	1	Membrane; single-pass type I membrane protein				365
P22137 UniProt NPD GO	CLH_YEAST	Clathrin heavy chain	0.23	-	cyt	0	Cytoplasmic face of coated pits and vesicles	clathrin vesicle coat [TAS]			1653
Q6DJE4 UniProt NPD GO	CPSF5_XENLA	Cleavage and polyadenylation specificity factor 5	0.23	-	mit	0	Nucleus (By similarity)	paraspeckles [ISS]			227
Q5ZL57 UniProt NPD GO	COPD_CHICK	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.23	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				510
Q9W6X0 UniProt NPD GO	NXSH_NAJAT	Cobrotoxin homolog precursor	0.23	-	nuc	0	Secreted protein				82
Q9PTT0 UniProt NPD GO	NXSH_NAJNA	Cobrotoxin homolog precursor	0.23	-	nuc	0	Secreted protein				83
P60770 UniProt NPD GO	NXS1_NAJAT	Cobrotoxin precursor (CBT) (Short neurotoxin 1)	0.23	-	nuc	0	Secreted protein			1V6P	83
P45594 UniProt NPD GO	CADF_DROME	Cofilin/actin-depolymerizing factor homolog (Protein D61) (Protein twinstar)	0.23	+	nuc	0	Nucleus (Potential)				148
Q9Y3C0 UniProt NPD GO	CCD53_HUMAN	Coiled-coil domain-containing protein 53	0.23	-	nuc	0					194
Q7SIB2 UniProt NPD GO	CO4A1_BOVIN	Collagen alpha-1(IV) chain (Fragment)	0.23	-	nuc	0				1M3D	229
Q28083 UniProt NPD GO	COBA1_BOVIN	Collagen alpha-1(XI) chain precursor (Fragment)	0.23	-	nuc	0					911

You are viewing entries 47201 to 47250 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.