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
Q27793 UniProt NPD GO	DRTS_TRYCR	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.17	-	cyt	0					521
Q9GKQ6 UniProt NPD GO	PGS1_PIG	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1) (Fragments)	0.17	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				272
P07952 UniProt NPD GO	PMGE_RABIT	Bisphosphoglycerate mutase (EC 5.4.2.4) (2,3-bisphosphoglycerate mutase, erythrocyte) (2,3-bisphosph ...	0.17	-	cyt	0					258
P01059 UniProt NPD GO	IBB4_DOLAX	Bowman-Birk type proteinase inhibitor DE-4	0.17	-	nuc	0				1GM2	76
P01022 UniProt NPD GO	BPP2_BOTJA	Bradykinin-potentiating peptide V-6-II (Angiotensin-converting enzyme inhibitor V-6-II)	0.17	-		0					10
O95415 UniProt NPD GO	BI3_HUMAN	Brain protein I3 (pRGR2)	0.17	-	nuc	2					125
Q8L493 UniProt NPD GO	BCAL3_ARATH	Branched-chain-amino-acid aminotransferase-like protein 3, chloroplast precursor	0.17	-	mit	0	Plastid; chloroplast (Potential)				373
Q05004 UniProt NPD GO	BB61_RABIT	Brush border protein AdRab-A precursor	0.17	-	exc	0					540
O62743 UniProt NPD GO	CCR5_CERTO	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				352
O97962 UniProt NPD GO	CCR5_PYGAV	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				352
P61757 UniProt NPD GO	CCR5_SEMEN	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				352
O97878 UniProt NPD GO	CCR5_TRAFR	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				352
O97879 UniProt NPD GO	CCR5_TRAPH	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				352
Q9D8X5 UniProt NPD GO	CNOT8_MOUSE	CCR4-NOT transcription complex subunit 8 (CCR4-associated factor 8)	0.17	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				292
Q9Z2V2 UniProt NPD GO	CD40L_RAT	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.17	+	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			260
P48960 UniProt NPD GO	CD97_HUMAN	CD97 antigen precursor (Leukocyte antigen CD97)	0.17	-	end	7	Cell membrane; multi-pass membrane protein. Subunit alpha: Secreted protein; extracellular space. A ...	integral to plasma membrane [TAS] plasma membrane [TAS]	601211		835
Q11200 UniProt NPD GO	SIA4A_CHICK	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.4) (Beta-galactosi ...	0.17	+	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				342
Q92182 UniProt NPD GO	SIAT1_CHICK	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase (EC 2.4.99.1) (Beta-galactosi ...	0.17	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	integral to membrane [ISS]			413
P28274 UniProt NPD GO	URA7_YEAST	CTP synthase 1 (EC 6.3.4.2) (UTP--ammonia ligase 1) (CTP synthetase 1)	0.17	-	cyt	0		cytosol [TAS]			579
P50547 UniProt NPD GO	PYRG1_CRIGR	CTP synthase 1 (EC 6.3.4.2) (UTP--ammonia ligase 1) (CTP synthetase 1) (Fragment)	0.17	-	cyt	0					447
P97291 UniProt NPD GO	CADH8_MOUSE	Cadherin-8 precursor	0.17	-	nuc	1	Membrane; single-pass type I membrane protein			2A62	799
P53806 UniProt NPD GO	CCPL_CAEEL	Calcipressin-like protein (Down syndrome candidate region 1-like protein)	0.17	-	nuc	0					207
Q91YS8 UniProt NPD GO	KCC1A_MOUSE	Calcium/calmodulin-dependent protein kinase type 1 (EC 2.7.11.17) (CaM kinase I) (CaM-KI) (CaM kinas ...	0.17	-	cyt	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity)	calcium- and calmodulin-dependent protein k... [TAS]			374
Q63450 UniProt NPD GO	KCC1A_RAT	Calcium/calmodulin-dependent protein kinase type 1 (EC 2.7.11.17) (CaM kinase I) (CaM-KI) (CaM kinas ...	0.17	-	cyt	0	Cytoplasm. Predominantly. Nucleus	calcium- and calmodulin-dependent protein k... [TAS]		1MXE	374
Q16566 UniProt NPD GO	KCC4_HUMAN	Calcium/calmodulin-dependent protein kinase type IV (EC 2.7.11.17) (CAM kinase-GR) (CaMK IV)	0.17	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Substantial localization in certain neuronal nuc ...		114080		473
P10463 UniProt NPD GO	CAYP1_CANFA	Calcyphosin (Calcyphosine) (Thyroid protein p24) (TPP) (Protein 5)	0.17	-	cyt	0	Cytoplasm				189
Q9D7J7 UniProt NPD GO	CPNS2_MOUSE	Calpain small subunit 2 (CSS2) (Calcium-dependent protease small subunit 2)	0.17	-	mit	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon c ...				247
Q99JH7 UniProt NPD GO	CSTN3_MOUSE	Calsyntenin-3 precursor	0.17	-	end	1	Membrane; single-pass type I membrane protein (Potential)	postsynaptic membrane [IDA]			956
Q9Y2D0 UniProt NPD GO	CAH5B_HUMAN	Carbonic anhydrase 5B, mitochondrial precursor (EC 4.2.1.1) (Carbonic anhydrase VB) (Carbonate dehyd ...	0.17	-	mit	0	Mitochondrion	mitochondrion [TAS]	300230		317
P27614 UniProt NPD GO	CBPS_YEAST	Carboxypeptidase S (EC 3.4.17.4) (YSCS) (GLY-X carboxypeptidase)	0.17	-	mit	1 *	Vacuole. Lysosome-like vacuoles	vacuole (sensu Fungi) [TAS]			576
Q9PT92 UniProt NPD GO	CATA_BRARE	Catalase (EC 1.11.1.6)	0.17	-	cyt	0	Peroxisome (By similarity)				526
O62839 UniProt NPD GO	CATA_PIG	Catalase (EC 1.11.1.6)	0.17	-	cyt	0	Peroxisome (By similarity)				526
O24339 UniProt NPD GO	CATA_SOLAP	Catalase (EC 1.11.1.6)	0.17	-	cyt	0	Peroxisome (By similarity)				492
P29611 UniProt NPD GO	CATA1_ORYSA	Catalase isozyme A (EC 1.11.1.6) (CAT-A)	0.17	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)	glyoxysome [IDA] peroxisome [IDA]			492
P61276 UniProt NPD GO	CATK_MACFA	Cathepsin K precursor (EC 3.4.22.38)	0.17	-	end	0	Lysosome (By similarity)				329
P61277 UniProt NPD GO	CATK_MACMU	Cathepsin K precursor (EC 3.4.22.38)	0.17	-	end	0	Lysosome (By similarity)				329
P23572 UniProt NPD GO	CDC2_DROME	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase)	0.17	-	cyt	0	Nucleus (By similarity)				297
P54664 UniProt NPD GO	CC2H1_TRYCO	Cell division control protein 2 homolog 1 (EC 2.7.11.22)	0.17	-	cyt	0					301
Q05006 UniProt NPD GO	CDC22_MEDSA	Cell division control protein 2 homolog 2 (EC 2.7.11.22)	0.17	-	cyt	0					294
P28567 UniProt NPD GO	CDC22_PEA	Cell division control protein 2 homolog 2 (EC 2.7.11.22) (EC 2.7.11.23) (Fragment)	0.17	-	cyt	0					151
Q00534 UniProt NPD GO	CDK6_HUMAN	Cell division protein kinase 6 (EC 2.7.11.22) (Serine/threonine-protein kinase PLSTIRE)	0.17	-	cyt	0			603368	1XO2	326
Q05777 UniProt NPD GO	YL194_YEAST	Cell wall protein YLR194C precursor	0.17	-	exc	0	Cell wall; lipid-anchor; GPI-anchor. GPI-anchored cell wall protein (GPI-CWP)	anchored to plasma membrane [IDA] cell wall (sensu Fungi) [IDA]			254
O74683 UniProt NPD GO	KRE9_CANGA	Cell wall synthesis protein KRE9 precursor	0.17	-	vac	0	Cell surface (By similarity). Secreted, probably found at cell surface (By similarity)				276
P49449 UniProt NPD GO	CENPA_BOVIN	Centromere protein A (CENP-A) (Centromere autoantigen A) (Fragment)	0.17	-	mit	0	Nucleus				93
O55233 UniProt NPD GO	CER1_MOUSE	Cerberus precursor (Cerberus-related protein) (Cerberus-like protein) (Cer-l)	0.17	-	exc	0	Secreted protein	extracellular region [IDA]			272
P48405 UniProt NPD GO	CHSY_ORYSA	Chalcone synthase (EC 2.3.1.74) (Naregenin-chalcone synthase)	0.17	-	cyt	0					398
P48390 UniProt NPD GO	CHS1_GERHY	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.17	-	nuc	0					398
Q37106 UniProt NPD GO	DNAK_CYAPA	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.17	-	cyt	0	Plastid; cyanelle				623
P83630 UniProt NPD GO	CB30_HYDMC	Chitin-binding protein HM30 (Fragment)	0.17	-		0					15
P92941 UniProt NPD GO	CLCA_ARATH	Chloride channel protein CLC-a (AtCLC-a)	0.17	-	end	11	Membrane; multi-pass membrane protein				775

You are viewing entries 54101 to 54150 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.