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
Q9D8S9 UniProt NPD GO	BOLA1_MOUSE	BolA-like protein 1	0.29	-	nuc	0				1V60	137
Q9H3K6 UniProt NPD GO	BOLA2_HUMAN	BolA-like protein 2	0.29	-	cyt	0					86
P22737 UniProt NPD GO	IBB3_SETIT	Bowman-Birk type trypsin inhibitor 3 (Bowman-Birk type trypsin inhibitor III) (FMTI-III)	0.29	-	nuc	0					67
O15178 UniProt NPD GO	BRAC_HUMAN	Brachyury protein (T protein)	0.29	-	nuc	0	Nucleus		601397		435
P80723 UniProt NPD GO	BASP_HUMAN	Brain acid soluble protein 1 (BASP1 protein) (Neuronal axonal membrane protein NAP-22) (22 kDa neuro ...	0.29	-	nuc	0	Membrane; lipid-anchor. Associated with the membranes of "growth cones" that form the tips of elonga ...	cytoskeleton [TAS] plasma membrane [TAS]	605940		226
Q9AWM9 UniProt NPD GO	BXDC1_ORYSA	Brix domain-containing protein 1 homolog	0.29	-	nuc	0	Nucleus; nucleolus (By similarity)				310
P29773 UniProt NPD GO	ETS2_LYTVA	C-ets-2 protein (Fragment)	0.29	+	nuc	0	Nucleus				110
Q28008 UniProt NPD GO	CLC3A_BOVIN	C-type lectin domain family 3 member A precursor (C-type lectin superfamily member 1) (Cartilage-der ...	0.29	-	vac	0					197
Q8WMD0 UniProt NPD GO	COMD1_CANFA	COMM domain-containing protein 1 (Protein Murr1)	0.29	-	cyt	0					188
Q6GQA6 UniProt NPD GO	CSN8_XENLA	COP9 signalosome complex subunit 8 (Signalosome subunit 8)	0.29	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				195
P12400 UniProt NPD GO	CTL2B_MOUSE	CTLA-2-beta protein precursor (Fragment)	0.29	-	nuc	0					141
P55289 UniProt NPD GO	CAD12_HUMAN	Cadherin-12 precursor (Brain-cadherin) (BR-cadherin) (N-cadherin 2) (Neural type cadherin 2)	0.29	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	600562		794
P55291 UniProt NPD GO	CAD15_HUMAN	Cadherin-15 precursor (Muscle-cadherin) (M-cadherin) (Cadherin-14)	0.29	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	114019		814
Q99PF4 UniProt NPD GO	CAD23_MOUSE	Cadherin-23 precursor (Otocadherin)	0.29	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				3354
P58365 UniProt NPD GO	CAD23_RAT	Cadherin-23 precursor (Otocadherin)	0.29	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				3317
P53805 UniProt NPD GO	CCP1_HUMAN	Calcipressin-1 (Down syndrome critical region protein 1) (Myocyte-enriched calcineurin-interacting p ...	0.29	-	nuc	0		nucleus [TAS]	602917		197
O35427 UniProt NPD GO	CRCP_MOUSE	Calcitonin gene-related peptide-receptor component protein (CGRP-receptor component protein) (CGRP-R ...	0.29	-	nuc	0		acrosome [IDA]			148
Q9QYK9 UniProt NPD GO	KCC1B_MOUSE	Calcium/calmodulin-dependent protein kinase type 1B (EC 2.7.11.17) (CaM kinase IB) (CaM kinase I bet ...	0.29	-	mit	0	Cytoplasm. Nucleus	calcium- and calmodulin-dependent protein k... [TAS]			343
P28652 UniProt NPD GO	KCC2B_MOUSE	Calcium/calmodulin-dependent protein kinase type II beta chain (EC 2.7.11.17) (CaM-kinase II beta ch ...	0.29	-	mit	0		calcium- and calmodulin-dependent protein k... [TAS]			542
P15791 UniProt NPD GO	KCC2D_RAT	Calcium/calmodulin-dependent protein kinase type II delta chain (EC 2.7.11.17) (CaM-kinase II delta ...	0.29	-	mit	0		calcium- and calmodulin-dependent protein k... [TAS] cytosol [IPI]			533
Q5NVS7 UniProt NPD GO	CAN1_PONPY	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.29	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				714
O35646 UniProt NPD GO	CAN6_MOUSE	Calpain-6	0.29	-	nuc	0					641
Q9Y6Q1 UniProt NPD GO	CAN6_HUMAN	Calpain-6 (Calpamodulin) (CalpM) (Calpain-like protease X-linked)	0.29	-	nuc	0			300146		641
Q08094 UniProt NPD GO	CNN2_PIG	Calponin-2 (Calponin H2, smooth muscle) (Neutral calponin) (Fragment)	0.29	-	nuc	0					296
Q9V498 UniProt NPD GO	CSTN1_DROME	Calsyntenin-1 precursor	0.29	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	extracellular region [ISS] postsynaptic membrane [ISS]			978
O94985 UniProt NPD GO	CSTN1_HUMAN	Calsyntenin-1 precursor	0.29	-	end	1	Membrane; single-pass type I membrane protein (Potential)				981
P25421 UniProt NPD GO	TKNC_CARAU	Carassin	0.29	-	nuc	0	Secreted protein				21
O94313 UniProt NPD GO	CARB_SCHPO	Carbamoyl-phosphate synthase arginine-specific large chain (EC 6.3.5.5) (Arginine-specific carbamoyl ...	0.29	-	cyt	0	Cytoplasm (By similarity)				1160
P51201 UniProt NPD GO	CARA_PORPU	Carbamoyl-phosphate synthase small chain (EC 6.3.5.5) (Carbamoyl-phosphate synthetase glutamine chai ...	0.29	-	cyt	0	Plastid; chloroplast				384
Q80WV3 UniProt NPD GO	CHST2_MOUSE	Carbohydrate sulfotransferase 2 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 1) (GlcNAc6ST ...	0.29	-	mit	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type II membrane pro ...				530
Q8NCH0 UniProt NPD GO	CHSTE_HUMAN	Carbohydrate sulfotransferase D4ST1 (EC 2.8.2.-) (Dermatan 4-sulfotransferase 1) (D4ST-1) (hD4ST)	0.29	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [ISS]	608429		376
Q64444 UniProt NPD GO	CAH4_MOUSE	Carbonic anhydrase 4 precursor (EC 4.2.1.1) (Carbonic anhydrase IV) (Carbonate dehydratase IV) (CA-I ...	0.29	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)			3ZNC	305
Q9JJN5 UniProt NPD GO	CBPN_MOUSE	Carboxypeptidase N catalytic chain precursor (EC 3.4.17.3) (CPN) (Carboxypeptidase N polypeptide 1) ...	0.29	-	mit	0	Secreted protein; extracellular space				457
Q9QZM3 UniProt NPD GO	CLCF1_MOUSE	Cardiotrophin-like cytokine factor 1 precursor (B cell-stimulating factor 3) (BSF-3) (Novel neurotro ...	0.29	-	mit	0	Secreted protein (By similarity)	extracellular region [ISS]			225
P97742 UniProt NPD GO	CPT1A_MOUSE	Carnitine O-palmitoyltransferase I, liver isoform (EC 2.3.1.21) (CPT I) (CPTI-L) (Carnitine palmitoy ...	0.29	-	end	2 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			773
Q58DK1 UniProt NPD GO	CPT1B_BOVIN	Carnitine O-palmitoyltransferase I, muscle isoform (EC 2.3.1.21) (CPT I) (CPTI-M) (Carnitine palmito ...	0.29	-	cyt	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				771
P04655 UniProt NPD GO	CAS2_CAVPO	Casein A precursor	0.29	-	exc	0	Secreted protein				223
O15726 UniProt NPD GO	KC1_PLAF4	Casein kinase I (EC 2.7.11.1)	0.29	-	cyt	0				1LHX	324
Q08466 UniProt NPD GO	CSK22_ARATH	Casein kinase II subunit alpha-2 (EC 2.7.11.1) (CK II)	0.29	-	cyt	0					333
P90682 UniProt NPD GO	CATA_ASCSU	Catalase (EC 1.11.1.6)	0.29	-	nuc	0	Peroxisome (By similarity)				541
P00432 UniProt NPD GO	CATA_BOVIN	Catalase (EC 1.11.1.6)	0.29	-	cyt	0	Peroxisome			8CAT	526
P17336 UniProt NPD GO	CATA_DROME	Catalase (EC 1.11.1.6)	0.29	-	pox	0	Peroxisome				506
P55305 UniProt NPD GO	CATA_EMENI	Catalase A (EC 1.11.1.6) (Spore-specific catalase)	0.29	-	cyt	0					744
P43157 UniProt NPD GO	CYSP_SCHJA	Cathepsin B-like cysteine proteinase precursor (EC 3.4.22.-) (Antigen Sj31)	0.29	-	end	0				1MF3	342
Q5PQP4 UniProt NPD GO	BORG1_RAT	Cdc42 effector protein 2 (Binder of Rho GTPases 1)	0.29	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)				214
P54665 UniProt NPD GO	CC2H2_TRYBB	Cell division control protein 2 homolog 2 (EC 2.7.11.22)	0.29	-	cyt	0					345
Q8R1U2 UniProt NPD GO	CGRE1_MOUSE	Cell growth regulator with EF hand domain 1 (Cell growth regulatory gene 11 protein)	0.29	-	exc	0					281
Q10303 UniProt NPD GO	ALP21_SCHPO	Cell polarity protein alp21 (Altered polarity protein 21) (Suppressor of tsm one protein 1)	0.29	-	cyt	0	Cytoplasm				511
P36627 UniProt NPD GO	BYR3_SCHPO	Cellular nucleic acid-binding protein homolog	0.29	-	nuc	0	Nucleus (Potential)				179
Q5RAU5 UniProt NPD GO	CHMP3_PONPY	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.29	-	nuc	0	Cytoplasm; cytosol. Membrane; lipid-anchor				221

You are viewing entries 41051 to 41100 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.