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
Q94557 UniProt NPD GO	CEC1_DROVI	Cecropin-1 precursor	0.05	-	vac	1 *	Secreted protein				63
P81686 UniProt NPD GO	CECB_DROMA	Cecropin-B precursor	0.05	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
Q38773 UniProt NPD GO	CDC2B_ANTMA	Cell division control protein 2 homolog B (EC 2.7.11.22) (EC 2.7.11.23) (Fragment)	0.05	-	cyt	0					280
O14426 UniProt NPD GO	CDC42_CANAL	Cell division control protein 42 homolog	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
P51166 UniProt NPD GO	CDK5_XENLA	Cell division protein kinase 5 (EC 2.7.11.22) (Neuronal cyclin-dependent kinase 5)	0.05	-	cyt	0		axon [ISS] cell soma [ISS] cytoplasm [ISS] dendrite [ISS] growth cone [ISS] membrane [ISS] neuromuscular junction [ISS] nucleus [ISS]			292
Q02399 UniProt NPD GO	CDK5_BOVIN	Cell division protein kinase 5 (EC 2.7.11.22) (Tau protein kinase II catalytic subunit) (TPKII catal ...	0.05	-	cyt	0	Cytoplasm. In axonal growth cone with extension to the peripheral lamellipodia (By similarity)	axon [ISS] cell soma [ISS] cytoplasm [ISS] dendrite [ISS] growth cone [ISS] membrane [ISS] neuromuscular junction [ISS] nucleus [ISS]			292
P81038 UniProt NPD GO	VSPA_CERCE	Cerastotin (EC 3.4.21.-) (Fragments)	0.05	-	cyt	0	Secreted protein				98
P51089 UniProt NPD GO	CHSY_VIGUN	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.05	-	nuc	0					388
Q9ZS41 UniProt NPD GO	CHS1_DAUCA	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1) (DcCHS1)	0.05	-	cyt	0					389
P48387 UniProt NPD GO	CHS2_CAMSI	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.05	-	cyt	0					389
Q42663 UniProt NPD GO	CFI_CALCH	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase) (Fragment)	0.05	-	cyt	0					237
P56281 UniProt NPD GO	CH60_LEITA	Chaperonin HSP60, mitochondrial precursor (Protein Cpn60) (groEL protein) (Heat shock protein 60) (F ...	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				47
P30593 UniProt NPD GO	CHS2_RHIAT	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-III chitin syn ...	0.05	-	mit	0	Cell membrane; multi-pass membrane protein				198
P40953 UniProt NPD GO	CHI2_CANAL	Chitinase 2 precursor (EC 3.2.1.14)	0.05	-	exc	0	Secreted protein (Probable)				583
P27520 UniProt NPD GO	CB23_PEA	Chlorophyll a-b binding protein 215, chloroplast precursor (LHCII type II CAB-215) (LHCP)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P27525 UniProt NPD GO	CB4B_LYCES	Chlorophyll a-b binding protein CP24 10B, chloroplast precursor (CAB-10B) (LHCP)	0.05	-	mit	2	Plastid; chloroplast				256
P14273 UniProt NPD GO	CB2_CHLRE	Chlorophyll a-b binding protein of LHCII type I, chloroplast precursor (CAB) (LHCP)	0.05	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				253
P27517 UniProt NPD GO	CB2_DUNTE	Chlorophyll a-b binding protein of LHCII type I, chloroplast precursor (CAB) (LHCP)	0.05	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				253
Q9LE89 UniProt NPD GO	CLH0_CHEAL	Chlorophyllase type 0 precursor (EC 3.1.1.14) (CaCLH0) (Chlorophyll-chlorophyllido hydrolase 0) (Chl ...	0.05	-	end	0					347
Q9MV14 UniProt NPD GO	CLH1_CITSI	Chlorophyllase-1, chloroplast precursor (EC 3.1.1.14) (Chlorophyll-chlorophyllido hydrolase 1) (Chla ...	0.05	-	mit	0	Plastid; chloroplast				329
Q94LX1 UniProt NPD GO	CLH1_CITUN	Chlorophyllase-1, chloroplast precursor (EC 3.1.1.14) (Chlorophyll-chlorophyllido hydrolase 1) (Chla ...	0.05	-	mit	0	Plastid; chloroplast (By similarity)				329
Q9MUU0 UniProt NPD GO	RR19_MESVI	Chloroplast 30S ribosomal protein S19	0.05	-	mit	0	Plastid; chloroplast				93
P52776 UniProt NPD GO	RR19_PINTH	Chloroplast 30S ribosomal protein S19	0.05	-	mit	0	Plastid; chloroplast				92
O98453 UniProt NPD GO	RR19_SPIMX	Chloroplast 30S ribosomal protein S19	0.05	-	nuc	0	Plastid; chloroplast				92
Q9TLU5 UniProt NPD GO	RR8_CYACA	Chloroplast 30S ribosomal protein S8	0.05	-	cyt	0	Plastid; chloroplast				133
P11094 UniProt NPD GO	RK14_CHLRE	Chloroplast 50S ribosomal protein L14	0.05	-	cyt	0	Plastid; chloroplast				122
P08529 UniProt NPD GO	RK14_MAIZE	Chloroplast 50S ribosomal protein L14	0.05	-	cyt	0	Plastid; chloroplast				123
P41633 UniProt NPD GO	RK14_PINTH	Chloroplast 50S ribosomal protein L14	0.05	-	cyt	0	Plastid; chloroplast				122
Q6L3G2 UniProt NPD GO	RK14_SACHY	Chloroplast 50S ribosomal protein L14	0.05	-	cyt	0	Plastid; chloroplast				123
Q6ENS7 UniProt NPD GO	RK14_SACOF	Chloroplast 50S ribosomal protein L14	0.05	-	cyt	0	Plastid; chloroplast				123
P06382 UniProt NPD GO	RK14_TOBAC	Chloroplast 50S ribosomal protein L14	0.05	-	cyt	0	Plastid; chloroplast				122
Q9TLT9 UniProt NPD GO	RK16_CYACA	Chloroplast 50S ribosomal protein L16	0.05	-	mit	0	Plastid; chloroplast				140
P42355 UniProt NPD GO	RK16_OENAM	Chloroplast 50S ribosomal protein L16 (Fragment)	0.05	-	mit	0	Plastid; chloroplast				90
P41552 UniProt NPD GO	RK27_PLEHA	Chloroplast 50S ribosomal protein L27 (Fragment)	0.05	-	cyt	0	Plastid; chloroplast				74
Q85FU0 UniProt NPD GO	RK31_CYAME	Chloroplast 50S ribosomal protein L31	0.05	-	cyt	0	Plastid; chloroplast				67
Q85FP7 UniProt NPD GO	CEMA_CYAME	Chloroplast envelope membrane protein	0.05	-	end	2	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				276
P46641 UniProt NPD GO	CEMA_MAIZE	Chloroplast envelope membrane protein	0.05	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				230
Q6L388 UniProt NPD GO	CEMA_SACHY	Chloroplast envelope membrane protein	0.05	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				230
Q6ENV2 UniProt NPD GO	CEMA_SACOF	Chloroplast envelope membrane protein	0.05	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				230
P59887 UniProt NPD GO	SCXL_BUTSI	Chlorotoxin-like peptide Bs 14 (Bs14)	0.05	-	nuc	0	Secreted protein				36
Q4G1G8 UniProt NPD GO	CH25H_PIG	Cholesterol 25-hydroxylase (EC 1.14.99.38) (Cholesterol 25-monooxygenase)	0.05	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				270
O95992 UniProt NPD GO	CH25H_HUMAN	Cholesterol 25-hydroxylase (EC 1.14.99.38) (Cholesterol 25-monooxygenase) (h25OH)	0.05	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)		604551		272
Q618G2 UniProt NPD GO	C25HL_CAEBR	Cholesterol 25-hydroxylase-like protein (EC 1.14.99.-)	0.05	-	cyt	3	Membrane; multi-pass membrane protein (Potential)				300
O77770 UniProt NPD GO	LECT1_RABIT	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) [Contain ...	0.05	-	cyt	1 *	Cytoplasm (By similarity). Secreted protein (By similarity). Accumulated in the inter-territorial ma ...				333
O70367 UniProt NPD GO	LECT1_RAT	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) [Contain ...	0.05	-	cyt	1 *	Cytoplasm (By similarity). Secreted protein (By similarity). Accumulated in the inter-territorial ma ...				334
Q6DG52 UniProt NPD GO	CHUR_MOUSE	Churchill protein	0.05	-	cyt	0					112
P00769 UniProt NPD GO	CTR2_VESCR	Chymotrypsin-2 (EC 3.4.21.1) (Chymotrypsin II)	0.05	-	cyt	0	Secreted protein; extracellular space				218
P00766 UniProt NPD GO	CTRA_BOVIN	Chymotrypsinogen A (EC 3.4.21.1) [Contains: Chymotrypsin A chain A; Chymotrypsin A chain B; Chymotry ...	0.05	-	cyt	0	Secreted protein; extracellular space			8GCH	245
Q71DR4 UniProt NPD GO	CNTFR_CANFA	Ciliary neurotrophic factor receptor alpha precursor (CNTFR alpha)	0.05	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				372
P26992 UniProt NPD GO	CNTFR_HUMAN	Ciliary neurotrophic factor receptor alpha precursor (CNTFR alpha)	0.05	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	extrinsic to membrane [TAS]	118946	1UC6	372

You are viewing entries 74051 to 74100 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.