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
Q3S4V6 UniProt NPD GO	IL4_AILME	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.18	-	mit	1 *	Secreted protein				132
Q04745 UniProt NPD GO	IL4_PIG	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.18	-	exc	0	Secreted protein				133
Q95181 UniProt NPD GO	IL6_HORSE	Interleukin-6 precursor (IL-6)	0.18	-	exc	0	Secreted protein				208
Q9P2H3 UniProt NPD GO	IFT80_HUMAN	Intraflagellar transport 80 homolog (WD repeat protein 56)	0.18	-	cyt	0					777
Q8K057 UniProt NPD GO	IFT80_MOUSE	Intraflagellar transport 80 homolog (WD repeat protein 56)	0.18	-	cyt	0					777
Q66HB3 UniProt NPD GO	IFT80_RAT	Intraflagellar transport 80 homolog (WD repeat protein 56)	0.18	-	cyt	0					777
P49656 UniProt NPD GO	IRK2_RABIT	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.18	-	mit	2	Membrane; multi-pass membrane protein				427
P09436 UniProt NPD GO	SYIC_YEAST	Isoleucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.18	-	cyt	0	Cytoplasm	cytosol [IDA]			1072
Q91167 UniProt NPD GO	NEU2_ONCKE	Isoticin-neurophysin IT 2 precursor [Contains: Isotocin (IT); Neurophysin IT 2]	0.18	-	nuc	0	Secreted protein				156
Q9DBJ6 UniProt NPD GO	JOS1_MOUSE	Josephin-1 (Josephin domain-containing protein 1)	0.18	-	mit	0					202
Q8AY56 UniProt NPD GO	NXKA_BUNCA	Kappa 1a-bungarotoxin precursor	0.18	-	nuc	0	Secreted protein (By similarity)				87
Q27952 UniProt NPD GO	CASK_BALPH	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				145
Q95146 UniProt NPD GO	CASK_CAPCA	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				123
Q95177 UniProt NPD GO	CASK_CERUN	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				122
Q95184 UniProt NPD GO	CASK_ELADA	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				122
Q95225 UniProt NPD GO	CASK_ODOHE	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				122
Q95228 UniProt NPD GO	CASK_ODOVI	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				122
Q95239 UniProt NPD GO	CASK_RANTA	Kappa-casein (Fragment)	0.18	-	mit	0	Secreted protein				122
P19442 UniProt NPD GO	CASK_CAVPO	Kappa-casein precursor	0.18	-	nuc	0	Secreted protein				234
Q9BQ90 UniProt NPD GO	KLDC3_HUMAN	Kelch domain-containing protein 3 (Protein Peas) (Testis intracellular mediator protein)	0.18	-	cyt	0	Cytoplasm. Also found in meiotic chromatin (By similarity)	cytoplasm [IDA] nuclear chromatin [IDA]			382
Q8WZ60 UniProt NPD GO	KLHL6_HUMAN	Kelch-like protein 6	0.18	-	cyt	0					610
Q9P2G9 UniProt NPD GO	KLHL8_HUMAN	Kelch-like protein 8	0.18	-	nuc	0					620
P04260 UniProt NPD GO	K2C4_BOVIN	Keratin, type II cytoskeletal 59 kDa, component IV (Keratin K6 gamma) (Fragment)	0.18	-	nuc	0					182
P59990 UniProt NPD GO	KR121_HUMAN	Keratin-associated protein 12-1 (Keratin-associated protein 12.1) (High sulfur keratin-associated pr ...	0.18	-	mit	0					96
Q3LI59 UniProt NPD GO	KR212_HUMAN	Keratin-associated protein 21-2	0.18	-	nuc	0					83
P01045 UniProt NPD GO	KNG2_BOVIN	Kininogen-2 precursor (Kininogen II) (Thiol proteinase inhibitor) [Contains: Kininogen-2 heavy chain ...	0.18	-	exc	0	Secreted protein; extracellular space				619
P79288 UniProt NPD GO	KLF9_PIG	Krueppel-like factor 9 (Transcription factor BTEB1) (Basic transcription element-binding protein 1) ...	0.18	-	nuc	0	Nucleus				138
P81548 UniProt NPD GO	AXP2_ANTAF	Kunitz-type proteinase inhibitor AXPI-II	0.18	-	nuc	0	Secreted protein. Found in nematocyst				58
P70712 UniProt NPD GO	KYNU_RAT	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.18	-	cyt	0	Cytoplasm				464
Q8BQ89 UniProt NPD GO	LIX1L_MOUSE	LIX1-like protein	0.18	-	nuc	0					337
Q8L8Q3 UniProt NPD GO	LBD25_ARATH	LOB domain-containing protein 25	0.18	-	nuc	0					159
Q9SA51 UniProt NPD GO	LBD3_ARATH	LOB domain-containing protein 3	0.18	-	mit	0					165
P70490 UniProt NPD GO	MFGM_RAT	Lactadherin precursor (Milk fat globule-EGF factor 8) (MFG-E8) (O-acetyl GD3 ganglioside synthase) ( ...	0.18	-	exc	0	Membrane; peripheral membrane protein				427
Q6Q4G3 UniProt NPD GO	LAEVR_HUMAN	Laeverin (EC 3.4.-.-) (CHL2 antigen)	0.18	-	mit	1 *	Membrane; single-pass type II membrane protein		610046		989
O43813 UniProt NPD GO	LANC1_HUMAN	LanC-like protein 1 (40 kDa erythrocyte membrane protein) (p40)	0.18	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein	integral to plasma membrane [TAS]	604155		399
Q9AYP9 UniProt NPD GO	LECC_PHYAM	Lectin-C precursor (PL-C)	0.18	-	exc	1 *				1ULK	194
Q4V8D9 UniProt NPD GO	LRC34_RAT	Leucine-rich repeat-containing protein 34	0.18	-	nuc	0					415
P10857 UniProt NPD GO	SYLC_NEUCR	Leucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.18	-	cyt	0	Cytoplasm				1123
O43262 UniProt NPD GO	LEU2_HUMAN	Leukemia-associated protein 2 (Deleted in lymphocytic leukemia 2)	0.18	-	nuc	0			605766		84
Q3SZH7 UniProt NPD GO	LKHA4_BOVIN	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.18	-	cyt	0	Cytoplasm (By similarity)				610
P09960 UniProt NPD GO	LKHA4_HUMAN	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.18	-	cyt	0	Cytoplasm		151570	1SQM	610
Q85AC2 UniProt NPD GO	CHLB_ANTFO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.18	-	cyt	0	Plastid; chloroplast				513
P37824 UniProt NPD GO	CHLB_CHLPT	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.18	-	cyt	0	Plastid; chloroplast				444
P41498 UniProt NPD GO	PPAC_RAT	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (LMW-PTP) (Low molecular weig ...	0.18	-	nuc	0	Cytoplasm	synaptosome [IDA]			157
Q04504 UniProt NPD GO	LA_RABIT	Lupus La protein homolog (La ribonucleoprotein) (La autoantigen homolog) (Fragment)	0.18	-	nuc	0	Nucleus (Probable)				53
Q66H42 UniProt NPD GO	LYPD1_RAT	Ly6/PLAUR domain-containing protein 1 precursor	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				141
P10619 UniProt NPD GO	PPGB_HUMAN	Lysosomal protective protein precursor (EC 3.4.16.5) (Cathepsin A) (Carboxypeptidase C) (Protective ...	0.18	-	gol	0	Lysosome	endoplasmic reticulum [TAS] lysosome [NAS]	256540	1IVY	480
Q6GNY7 UniProt NPD GO	PPT2B_XENLA	Lysosomal thioesterase PPT2-B precursor (EC 3.1.2.-) (PPT-2-B)	0.18	-	end	0	Lysosome (By similarity)				288
Q05820 UniProt NPD GO	LYSC2_RAT	Lysozyme C type 2 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.18	-	exc	0					148
O49873 UniProt NPD GO	MLOH1_HORVU	MLO protein homolog 1	0.18	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				544

You are viewing entries 53201 to 53250 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.