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
Q9NY30 UniProt NPD GO	BTG4_HUMAN	BTG4 protein (PC3b)	0.45	-	nuc	0			605673		223
P98160 UniProt NPD GO	PGBM_HUMAN	Basement membrane-specific heparan sulfate proteoglycan core protein precursor (HSPG) (Perlecan) (PL ...	0.45	-	nuc	0	Secreted protein; extracellular space		255800		4391
Q95JC9 UniProt NPD GO	PRP_PIG	Basic proline-rich protein precursor [Contains: Proline-rich peptide SP-A (PRP-SP-A); Proline-rich p ...	0.45	+	exc	0	Secreted protein				676
Q92934 UniProt NPD GO	BAD_HUMAN	Bcl2 antagonist of cell death (BAD) (Bcl-2-binding component 6) (Bcl-XL/Bcl-2-associated death promo ...	0.45	-	nuc	0	Mitochondrion; mitochondrial outer membrane. Cytoplasm. Upon phosphorylation, locates to the cytopla ...	cytoplasm [NAS] mitochondrial outer membrane [NAS]	603167	1G5J	168
Q9Y644 UniProt NPD GO	RFNG_HUMAN	Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.45	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	extracellular region [NAS]	602578		331
Q9GKK3 UniProt NPD GO	CASB_HORSE	Beta-casein precursor	0.45	-	exc	0	Secreted protein				241
Q7Z7B7 UniProt NPD GO	DB132_HUMAN	Beta-defensin 132 precursor (Defensin, beta 132) (Beta-defensin 32) (DEFB-32) (BD-32)	0.45	-	exc	0	Secreted protein (Potential)				95
Q70KL3 UniProt NPD GO	BD39_MOUSE	Beta-defensin 39 precursor (Defensin, beta 39) (BD-39) (mBD-39)	0.45	-	nuc	0	Secreted protein (By similarity)				74
P35070 UniProt NPD GO	BTC_HUMAN	Betacellulin precursor (BTC)	0.45	+	end	2 *	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...	soluble fraction [TAS]	600345	1IP0	178
Q04757 UniProt NPD GO	HR29_HALRO	Body wall muscle protein HR-29	0.45	-	nuc	0	Membrane; peripheral membrane protein				251
P41820 UniProt NPD GO	BFR1_SCHPO	Brefeldin A resistance protein	0.45	-	end	12	Membrane; multi-pass membrane protein				1530
Q9H8M2 UniProt NPD GO	BRD9_HUMAN	Bromodomain-containing protein 9 (Rhabdomyosarcoma antigen MU-RMS-40.8)	0.45	-	exc	0					501
P47855 UniProt NPD GO	ABEC1_RABIT	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1)	0.45	-	nuc	0					236
P49715 UniProt NPD GO	CEBPA_HUMAN	CCAAT/enhancer-binding protein alpha (C/EBP alpha)	0.45	+	nuc	0	Nucleus	nucleus [NAS]	116897		358
Q62192 UniProt NPD GO	CD180_MOUSE	CD180 antigen precursor (Lymphocyte antigen 78) (Radioprotective 105 kDa protein)	0.45	-	end	1	Cell membrane; single-pass type I membrane protein				661
Q99LM2 UniProt NPD GO	CK5P3_MOUSE	CDK5 regulatory subunit-associated protein 3	0.45	-	cyt	0					503
P13748 UniProt NPD GO	1A03_PANTR	CHLA class I histocompatibility antigen, A-108 alpha chain precursor	0.45	-	end	1	Membrane; single-pass type I membrane protein				365
Q9V345 UniProt NPD GO	CSN4_DROME	COP9 signalosome complex subunit 4 (Signalosome subunit 4) (Dch4)	0.45	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IMP]			407
Q9UUJ7 UniProt NPD GO	CSN7A_SCHPO	COP9 signalosome complex subunit 7A	0.45	+	cyt	0					205
P10287 UniProt NPD GO	CADH3_MOUSE	Cadherin-3 precursor (Placental-cadherin) (P-cadherin)	0.45	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			822
Q29RI6 UniProt NPD GO	CAB39_BOVIN	Calcium-binding protein 39	0.45	-	cyt	0	Cytoplasm (Potential)				341
Q9Y376 UniProt NPD GO	CAB39_HUMAN	Calcium-binding protein 39 (Protein Mo25)	0.45	-	cyt	0	Cytoplasm (Potential)			1UPL	341
Q7RAH3 UniProt NPD GO	CDPK1_PLAYO	Calcium-dependent protein kinase 1 (EC 2.7.11.1)	0.45	-	nuc	0	Membrane; lipid-anchor (By similarity). In the parasite and on erithrocytic membrane at a lower leve ...				534
Q06850 UniProt NPD GO	CDPK1_ARATH	Calcium-dependent protein kinase, isoform AK1 (EC 2.7.11.1) (CDPK)	0.45	-	cyt	0				2AAO	610
Q9GLG7 UniProt NPD GO	CAN3_MACFA	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.45	-	cyt	0	Cytoplasm (By similarity)				815
Q9Y6Z8 UniProt NPD GO	PALB_ASPOR	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease palB)	0.45	-	cyt	0					854
P16573 UniProt NPD GO	CEAM1_RAT	Carcinoembryonic antigen-related cell adhesion molecule 1 precursor (Cell-CAM 105) (C-CAM 105) (Ecto ...	0.45	-	nuc	1	Cell membrane; single-pass type I membrane protein. Canalicular domain of hepatocyte plasma membrane ...				519
Q98943 UniProt NPD GO	CASP2_CHICK	Caspase-2 precursor (EC 3.4.22.-) (CASP-2) (ICH-1 protease) (ICH-1L/1S) [Contains: Caspase-2 subunit ...	0.45	-	nuc	0					424
P30429 UniProt NPD GO	CED4_CAEEL	Cell death protein 4	0.45	-	cyt	0	Mitochondrion. In non cell death induced cells. Ced-9 is required for mitochondrial localization. Pe ...	cytosol [IDA] membrane fraction [IDA] perinuclear region [IDA] soluble fraction [IDA]		2A5Y	571
O74435 UniProt NPD GO	CDC31_SCHPO	Cell division control protein 31	0.45	-	mit	0	Nucleus. Associates with the half-bridge structure of the SPB	half bridge of spindle pole body [IDA]			176
Q12262 UniProt NPD GO	MCM16_YEAST	Central kinetochore subunit MCM16 (Minichromosome maintenance protein 16)	0.45	-	nuc	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA]			181
Q2TBN3 UniProt NPD GO	CETN2_BOVIN	Centrin-2	0.45	-	nuc	0	Centrosome. Centrosome of interphase and mitotic cells (By similarity)				172
O35648 UniProt NPD GO	CETN3_MOUSE	Centrin-3	0.45	-	nuc	0	Centrosome. Centrosome of interphase and mitotic cells	centriole [IDA]			167
Q60936 UniProt NPD GO	CABC1_MOUSE	Chaperone-activity of bc1 complex-like, mitochondrial precursor (Chaperone-ABC1-like)	0.45	-	cyt	0	Mitochondrion (By similarity)				645
Q5ZHN1 UniProt NPD GO	CHM2A_CHICK	Charged multivesicular body protein 2a (Chromatin-modifying protein 2a) (CHMP2a)	0.45	-	nuc	0	Cytoplasm; cytosol (By similarity)				220
Q5FW29 UniProt NPD GO	CHMP5_XENTR	Charged multivesicular body protein 5 (Chromatin-modifying protein 5)	0.45	-	nuc	0	Cytoplasm (By similarity)				219
P30602 UniProt NPD GO	CHS3_EXODE	Chitin synthase 3 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 3) (Class-III chitin syn ...	0.45	-	end	6	Cell membrane; multi-pass membrane protein				885
Q8MX32 UniProt NPD GO	IDGF3_DROSI	Chitinase-like protein Idgf3 precursor (Imaginal disk growth factor protein 3)	0.45	-	cyt	0	Secreted protein (By similarity). Secreted in hemolymph (By similarity). It is probably transported ...	extracellular region [ISS]			441
P35525 UniProt NPD GO	CLCN2_RAT	Chloride channel protein 2 (ClC-2)	0.45	-	end	11	Membrane; multi-pass membrane protein	actin cytoskeleton [ISS] insoluble fraction [ISS] microvillus [ISS]			907
Q6B8X8 UniProt NPD GO	RR12_GRATL	Chloroplast 30S ribosomal protein S12	0.45	-	nuc	0	Plastid; chloroplast				124
Q9TKZ7 UniProt NPD GO	RR12_NEPOL	Chloroplast 30S ribosomal protein S12	0.45	-	mit	0	Plastid; chloroplast				125
Q6EVZ3 UniProt NPD GO	RR15_NYMAL	Chloroplast 30S ribosomal protein S15	0.45	-	nuc	0	Plastid; chloroplast				87
Q8WI27 UniProt NPD GO	RR2_PSINU	Chloroplast 30S ribosomal protein S2	0.45	-	cyt	0	Plastid; chloroplast				239
Q3V532 UniProt NPD GO	RR4_ACOCL	Chloroplast 30S ribosomal protein S4	0.45	-	mit	0	Plastid; chloroplast				201
P59135 UniProt NPD GO	RR4_BRYCA	Chloroplast 30S ribosomal protein S4	0.45	-	mit	0	Plastid; chloroplast				202
Q9M4B9 UniProt NPD GO	RR4_DIPFO	Chloroplast 30S ribosomal protein S4	0.45	-	mit	0	Plastid; chloroplast				202
P59141 UniProt NPD GO	RR4_HYPAR	Chloroplast 30S ribosomal protein S4	0.45	-	mit	0	Plastid; chloroplast				202
Q9FSE4 UniProt NPD GO	RR4_PLAAD	Chloroplast 30S ribosomal protein S4	0.45	-	mit	0	Plastid; chloroplast				202
O20210 UniProt NPD GO	RR4_DIERO	Chloroplast 30S ribosomal protein S4 (Fragment)	0.45	-	mit	0	Plastid; chloroplast				182
P36472 UniProt NPD GO	RR4_STICA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.45	-	mit	0	Plastid; chloroplast				196

You are viewing entries 28151 to 28200 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.