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
Q12018 UniProt NPD GO	CDC53_YEAST	Cell division control protein 53 (Cullin-A) (E3 ubiquitin ligase complex SCF subunit CDC53)	0.57	-	cyt	0	Cytoplasm. Nucleus	nuclear ubiquitin ligase complex [TAS] SCF ubiquitin ligase complex [IDA]			815
Q12215 UniProt NPD GO	WSC3_YEAST	Cell wall integrity and stress response component 3 precursor	0.57	-	nuc	2 *					556
Q99126 UniProt NPD GO	CHSX_USTMA	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1)	0.57	-	end	4	Cell membrane; multi-pass membrane protein				760
Q9GGE2 UniProt NPD GO	RR14_CHLRE	Chloroplast 30S ribosomal protein S14	0.57	-	mit	0	Plastid; chloroplast				100
Q3V4X7 UniProt NPD GO	RR15_ACOCL	Chloroplast 30S ribosomal protein S15	0.57	-	nuc	0	Plastid; chloroplast				90
Q49KU1 UniProt NPD GO	RR15_EUCGG	Chloroplast 30S ribosomal protein S15	0.57	-	nuc	0	Plastid; chloroplast				91
Q9BBN7 UniProt NPD GO	RR15_LOTJA	Chloroplast 30S ribosomal protein S15	0.57	-	nuc	0	Plastid; chloroplast				90
P30389 UniProt NPD GO	RR2_EUGGR	Chloroplast 30S ribosomal protein S2	0.57	-	mit	0	Plastid; chloroplast				240
P36466 UniProt NPD GO	RR4_MELUN	Chloroplast 30S ribosomal protein S4 (Fragment)	0.57	-	mit	0	Plastid; chloroplast				196
O47029 UniProt NPD GO	RR4_NAROD	Chloroplast 30S ribosomal protein S4 (Fragment)	0.57	-	mit	0	Plastid; chloroplast				196
Q6B8X9 UniProt NPD GO	RR7_GRATL	Chloroplast 30S ribosomal protein S7	0.57	-	nuc	0	Plastid; chloroplast				156
Q6EM90 UniProt NPD GO	RR7_HOUCO	Chloroplast 30S ribosomal protein S7	0.57	-	nuc	0	Plastid; chloroplast				155
Q33BZ7 UniProt NPD GO	RR8_NICTO	Chloroplast 30S ribosomal protein S8	0.57	-	nuc	0	Plastid; chloroplast				134
P56357 UniProt NPD GO	RK32_CHLVU	Chloroplast 50S ribosomal protein L32	0.57	-	nuc	0	Plastid; chloroplast				57
Q5SD38 UniProt NPD GO	CEMA_HUPLU	Chloroplast envelope membrane protein	0.57	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				521
O08786 UniProt NPD GO	CCKAR_MOUSE	Cholecystokinin type A receptor (CCK-A receptor) (CCK-AR) (Cholecystokinin-1 receptor) (CCK1-R)	0.57	-	end	7 *	Membrane; multi-pass membrane protein				436
Q5BBV4 UniProt NPD GO	EAF3_EMENI	Chromatin modification-related protein eaf3	0.57	-	nuc	0	Nucleus (By similarity)				327
P45973 UniProt NPD GO	CBX5_HUMAN	Chromobox protein homolog 5 (Heterochromatin protein 1 homolog alpha) (HP1 alpha) (Antigen p25)	0.57	+	nuc	0	Nucleus. Component of centromeric and pericentromeric heterochromatin. Associates with chromosomes d ...	nuclear envelope [TAS] nuclear heterochromatin [TAS]	604478		191
Q95KN1 UniProt NPD GO	CLUL1_CANFA	Clusterin-like protein 1 precursor (Retinal-specific clusterin-like protein)	0.57	-	exc	0	Secreted protein (Probable)				465
O60826 UniProt NPD GO	CCD22_HUMAN	Coiled-coil domain-containing protein 22	0.57	-	nuc	0					627
Q3ZC50 UniProt NPD GO	CCD47_BOVIN	Coiled-coil domain-containing protein 47 precursor	0.57	-	end	0	Membrane; single-pass membrane protein (Potential)				483
Q8BYH3 UniProt NPD GO	CCD76_MOUSE	Coiled-coil domain-containing protein 76	0.57	-	cyt	0					481
Q9D8L5 UniProt NPD GO	CCD91_MOUSE	Coiled-coil domain-containing protein 91 (GGA-binding partner)	0.57	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Golgi apparatus; trans-Golgi network; trans-G ...				442
Q9CQA6 UniProt NPD GO	CHCH1_MOUSE	Coiled-coil-helix-coiled-coil-helix domain-containing protein 1	0.57	-	mit	0	Nucleus (By similarity)				118
Q9NPY3 UniProt NPD GO	C1QR1_HUMAN	Complement component C1q receptor precursor (Complement component 1 q subcomponent receptor 1) (C1qR ...	0.57	+	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [IC]	120577		652
Q9TUQ3 UniProt NPD GO	CO7_PIG	Complement component C7 precursor	0.57	-	nuc	0					843
Q96JB2 UniProt NPD GO	COG3_HUMAN	Conserved oligomeric Golgi complex component 3 (Vesicle docking protein SEC34 homolog) (p94)	0.57	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Associated with the ...		606975		827
Q9VN14 UniProt NPD GO	CONT_DROME	Contactin precursor	0.57	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Component of epithelial septate junctions. Nrx is required ...	septate junction [IDA]			1390
P40512 UniProt NPD GO	CSN11_YEAST	Cop9 signalosome complex subunit 11 (Proteasome-COP9 signalosome-eIF3 domain protein 8)	0.57	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IDA]			444
Q13618 UniProt NPD GO	CUL3_HUMAN	Cullin-3 (CUL-3)	0.57	-	nuc	0	Nucleus. Golgi apparatus		603136		768
Q9JLV5 UniProt NPD GO	CUL3_MOUSE	Cullin-3 (CUL-3)	0.57	-	nuc	0	Nucleus. Golgi apparatus			1IUY	768
Q3TCH7 UniProt NPD GO	CUL4A_MOUSE	Cullin-4A (CUL-4A)	0.57	-	cyt	0					759
P48135 UniProt NPD GO	RR9_CYAPA	Cyanelle 30S ribosomal protein S9	0.57	-	nuc	0	Plastid; cyanelle				134
P18848 UniProt NPD GO	ATF4_HUMAN	Cyclic AMP-dependent transcription factor ATF-4 (Activating transcription factor 4) (DNA-binding pro ...	0.57	-	nuc	0	Nucleus	cytoplasm [ISS] nucleus [ISS]	604064	1CI6	351
Q92104 UniProt NPD GO	CP11B_RANCA	Cytochrome P450 11B, mitochondrial precursor (EC 1.14.15.4) (CYPXIB) (P450C11) (Steroid 11-beta-hydr ...	0.57	-	mit	0	Mitochondrion				517
O93323 UniProt NPD GO	CP26A_XENLA	Cytochrome P450 26A1 (EC 1.14.-.-) (Retinoic acid-degrading enzyme CYP26) (xCYP26) (Retinoic acid-co ...	0.57	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				492
P38818 UniProt NPD GO	CTM1_YEAST	Cytochrome c lysine N-methyltransferase 1 (EC 2.1.1.59)	0.57	-	cyt	0	Cytoplasm; cytosol	cytosol [IDA]			585
Q14008 UniProt NPD GO	CKAP5_HUMAN	Cytoskeleton-associated protein 5 (Colonic and hepatic tumor over-expressed protein) (Ch-TOG protein ...	0.57	-	end	0					2032
P20288 UniProt NPD GO	DRD2_BOVIN	D(2) dopamine receptor (Dopamine D2 receptor)	0.57	-	end	7 *	Membrane; multi-pass membrane protein				444
P34973 UniProt NPD GO	DRD2B_XENLA	D(2) dopamine receptor 2-B (D2R-B) (D2R 2) (Fragment)	0.57	-	end	5 *	Membrane; multi-pass membrane protein				345
O74372 UniProt NPD GO	DUO1_SCHPO	DASH complex subunit duo1 (Outer kinetochore protein duo1)	0.57	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)	DASH complex [IDA]			166
P26659 UniProt NPD GO	RAD15_SCHPO	DNA repair helicase rad15 (EC 3.6.1.-) (RAD3 homolog) (Protein rhp3)	0.57	-	cyt	0	Nucleus	nucleotide-excision repair factor 3 complex [IGI]			772
P55861 UniProt NPD GO	MCM2_XENLA	DNA replication licensing factor mcm2 (Minichromosome maintenance protein 2) (xMCM2) (BM28-homolog) ...	0.57	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			886
P49731 UniProt NPD GO	MCM6_SCHPO	DNA replication licensing factor mcm6 (Minichromosome maintenance protein 6)	0.57	-	mit	0	Nucleus (Potential)	MCM complex [IDA] nuclear chromatin [IDA]			892
Q8SSC4 UniProt NPD GO	RPB1_ENCCU	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1)	0.57	-	nuc	0	Nucleus (By similarity)				1599
Q6FLD5 UniProt NPD GO	RPB2_CANGA	DNA-directed RNA polymerase II polypeptide 2 (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.57	-	cyt	0	Nucleus (By similarity)				1223
P56762 UniProt NPD GO	RPOA_ARATH	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.57	-	mit	0	Plastid; chloroplast				329
Q8MAI6 UniProt NPD GO	RPOA_LOPEL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.57	-	cyt	0	Plastid; chloroplast				339
Q6ENE2 UniProt NPD GO	RPOA_ORYNI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.57	+	nuc	0	Plastid; chloroplast				337
P12090 UniProt NPD GO	RPOA_ORYSA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.57	+	nuc	0	Plastid; chloroplast				337

You are viewing entries 20651 to 20700 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.