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
Q9C124 UniProt NPD GO	ACEA_PICPA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.47	-	cyt	0	Peroxisome (By similarity)				550
P56633 UniProt NPD GO	CXK7A_CONPU	Kappa-conotoxin PVIIA precursor (Fin-popping peptide) (CGX-1051)	0.47	-	nuc	1 *	Secreted protein			1KCP	72
P25583 UniProt NPD GO	KAR4_YEAST	Karyogamy protein KAR4	0.47	-	nuc	0	Nucleus	nucleus [IC]			335
Q92764 UniProt NPD GO	K1H5_HUMAN	Keratin, type I cuticular Ha5 (Hair keratin, type I Ha5)	0.47	-	nuc	0			602764		425
P78386 UniProt NPD GO	KRHB5_HUMAN	Keratin, type II cuticular Hb5 (Hair keratin, type II Hb5)	0.47	-	mit	0			602767		507
Q6IFZ6 UniProt NPD GO	K2C1B_MOUSE	Keratin, type II cytoskeletal 1b (Type II keratin Kb39) (Embryonic type II keratin-1)	0.47	+	mit	0					572
Q9BQ66 UniProt NPD GO	KR412_HUMAN	Keratin-associated protein 4-12 (Keratin-associated protein 4.12) (Ultrahigh sulfur keratin-associat ...	0.47	-	nuc	0					201
Q9BYR3 UniProt NPD GO	KRA44_HUMAN	Keratin-associated protein 4-4 (Keratin-associated protein 4.4) (Ultrahigh sulfur keratin-associated ...	0.47	-	nuc	0					166
Q9BYR2 UniProt NPD GO	KRA45_HUMAN	Keratin-associated protein 4-5 (Keratin-associated protein 4.5) (Ultrahigh sulfur keratin-associated ...	0.47	-	nuc	0					186
Q3B7M5 UniProt NPD GO	LASP1_BOVIN	LIM and SH3 domain protein 1 (LASP-1)	0.47	-	nuc	0	Cytoplasm (By similarity). Associated with the F-actin rich cortical cytoskeleton (By similarity)				260
Q5R5W0 UniProt NPD GO	LASP1_PONPY	LIM and SH3 domain protein 1 (LASP-1)	0.47	-	nuc	0	Cytoplasm (By similarity). Associated with the F-actin rich cortical cytoskeleton (By similarity)				261
O77506 UniProt NPD GO	LASP1_RABIT	LIM and SH3 domain protein 1 (LASP-1) (40 kDa phosphoprotein) (pp40)	0.47	-	nuc	0	Cytoplasm (By similarity). Associated with the F-actin rich cortical cytoskeleton (By similarity)				263
O75112 UniProt NPD GO	LDB3_HUMAN	LIM domain-binding protein 3 (Z-band alternatively spliced PDZ-motif protein) (Protein cypher)	0.47	-	nuc	0	Localized to the cytoplasm around nuclei and pseudopodia of undifferentiated cells and detected thro ...	cytoskeleton [IDA]	115200	1RGW	727
Q8L5T5 UniProt NPD GO	LBD15_ARATH	LOB domain-containing protein 15	0.47	-	nuc	0					224
P09848 UniProt NPD GO	LPH_HUMAN	Lactase-phlorizin hydrolase precursor (Lactase-glycosylceramidase) [Includes: Lactase (EC 3.2.1.108) ...	0.47	-	nuc	1	Cell membrane; single-pass type I membrane protein. Brush border	integral to plasma membrane [TAS] membrane fraction [TAS]	603202		1927
Q00174 UniProt NPD GO	LAMA_DROME	Laminin alpha chain precursor	0.47	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basal lamina [IDA]			3712
Q01636 UniProt NPD GO	LAMBV_CHICK	Laminin beta-1 chain variant (Laminin beta-1-2 chain) (Fragment)	0.47	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component				198
O97817 UniProt NPD GO	LPHN2_BOVIN	Latrophilin-2 precursor (Calcium-independent alpha-latrotoxin receptor 2)	0.47	-	end	7	Membrane; multi-pass membrane protein				1478
O88923 UniProt NPD GO	LPHN2_RAT	Latrophilin-2 precursor (Calcium-independent alpha-latrotoxin receptor 2) (CIRL-2)	0.47	-	end	7	Membrane; multi-pass membrane protein				1487
O02671 UniProt NPD GO	LEPR_PIG	Leptin receptor precursor (LEP-R) (OB receptor) (OB-R) (CD295 antigen)	0.47	-	nuc	1 *	Membrane; single-pass type I membrane protein				1165
Q5XIN6 UniProt NPD GO	LETM1_RAT	Leucine zipper-EF-hand-containing transmembrane protein 1, mitochondrial precursor	0.47	-	nuc	1	Mitochondrion; mitochondrial membrane (By similarity)				739
Q8BGA3 UniProt NPD GO	LRTM2_MOUSE	Leucine-rich repeat transmembrane neuronal protein 2 precursor	0.47	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				515
O43155 UniProt NPD GO	FLRT2_HUMAN	Leucine-rich repeat transmembrane protein FLRT2 precursor (Fibronectin-like domain-containing leucin ...	0.47	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)	extracellular matrix (sensu Metazoa) [NAS] integral to plasma membrane [NAS]	604807		660
Q5RF01 UniProt NPD GO	LRC32_PONPY	Leucine-rich repeat-containing protein 32 precursor	0.47	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				662
Q14392 UniProt NPD GO	LRC32_HUMAN	Leucine-rich repeat-containing protein 32 precursor (GARP protein) (Garpin) (Glycoprotein A repetiti ...	0.47	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	137207		662
Q8N9N7 UniProt NPD GO	LRC57_HUMAN	Leucine-rich repeat-containing protein 57	0.47	-	nuc	0					239
Q93052 UniProt NPD GO	LPP_HUMAN	Lipoma-preferred partner (LIM domain-containing preferred translocation partner in lipoma)	0.47	-	nuc	0	Nucleus. Cytoplasm. Cell membrane; cell-cell junction. Cell membrane; cell-matrix junction. Found in ...		600700		612
Q91X13 UniProt NPD GO	LEAP2_CAVPO	Liver-expressed antimicrobial peptide 2 precursor (LEAP-2) (Fragment)	0.47	-	exc	0	Secreted protein				71
Q9D1Q1 UniProt NPD GO	MPH6_MOUSE	M-phase phosphoprotein 6	0.47	-	nuc	0	Nucleus; nucleolus (By similarity). Cytoplasm (By similarity). Cytoplasmic in M phase (By similarity ...				161
O24133 UniProt NPD GO	CHLD_TOBAC	Magnesium-chelatase subunit chlD, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.47	-	mit	0	Plastid; chloroplast; chloroplast stroma				758
Q6SJV8 UniProt NPD GO	CRD1_GOSHI	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase, chloroplast precursor (EC 1.14.13. ...	0.47	-	mit	0	Plastid; chloroplast (By similarity)				405
P10508 UniProt NPD GO	MAL63_YEAST	Maltose fermentation regulatory protein MAL63	0.47	-	nuc	0	Nucleus				473
P38287 UniProt NPD GO	CSH1_YEAST	Mannosyl phosphorylinositol ceramide synthase CSH1 (EC 2.-.-.-) (CSG1/SUR1 homolog 1)	0.47	-	end	3 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole (sensu Fungi) [IDA]			376
Q6QN06 UniProt NPD GO	MGP_CHILA	Matrix Gla-protein precursor (MGP)	0.47	-	exc	0	Secreted protein (By similarity)				103
Q9R0S2 UniProt NPD GO	MMP24_MOUSE	Matrix metalloproteinase-24 precursor (EC 3.4.24.-) (MMP-24) (Membrane-type matrix metalloproteinase ...	0.47	+	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. Also shed from ...				618
Q9TLD8 UniProt NPD GO	MATK_ANDPO	Maturase K (Intron maturase)	0.47	-	cyt	0	Plastid; chloroplast				506
Q9GHC3 UniProt NPD GO	MATK_LILRE	Maturase K (Intron maturase)	0.47	-	cyt	1	Plastid; chloroplast				512
Q9WTK8 UniProt NPD GO	SPO11_MOUSE	Meiotic recombination protein SPO11	0.47	-	cyt	0	Nucleus (By similarity)				396
Q8N7X4 UniProt NPD GO	MAGB6_HUMAN	Melanoma-associated antigen B6 (MAGE-B6 antigen)	0.47	-	nuc	0			300467		407
Q9HAY2 UniProt NPD GO	MAGF1_HUMAN	Melanoma-associated antigen F1 (MAGE-F1 antigen)	0.47	-	cyt	0					308
Q10268 UniProt NPD GO	MAC1_SCHPO	Membrane-anchored protein 1 precursor	0.47	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)	barrier septum [IDA] plasma membrane of cell tip [IDA]			756
P97772 UniProt NPD GO	MGR1_MOUSE	Metabotropic glutamate receptor 1 precursor (mGluR1)	0.47	-	end	7	Membrane; multi-pass membrane protein	cell soma [TAS] dendrite [IDA] postsynaptic membrane [TAS]			1199
Q9JIK9 UniProt NPD GO	RT34_MOUSE	Mitochondrial 28S ribosomal protein S34 (S34mt) (MRP-S34) (T-complex expressed gene 2 protein)	0.47	-	mit	0	Mitochondrion				218
P27927 UniProt NPD GO	RM16_MAIZE	Mitochondrial 60S ribosomal protein L16	0.47	-	mit	0	Mitochondrion				185
Q2UM43 UniProt NPD GO	GEM1_ASPOR	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.47	+	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				633
P40341 UniProt NPD GO	RCA1_YEAST	Mitochondrial respiratory chain complexes assembly protein RCA1 (EC 3.4.24.-) (TAT-binding homolog 1 ...	0.47	-	mit	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	cytoplasm [IDA] m-AAA complex [IDA] mitochondrion [IDA]			825
Q96008 UniProt NPD GO	RT12_ALLCE	Mitochondrial ribosomal protein S12	0.47	-	nuc	0	Mitochondrion				125
P07924 UniProt NPD GO	RT13_WHEAT	Mitochondrial ribosomal protein S13	0.47	-	nuc	0	Mitochondrion				116
Q9WTY9 UniProt NPD GO	MK13_RAT	Mitogen-activated protein kinase 13 (EC 2.7.11.24) (Stress-activated protein kinase 4) (Mitogen-acti ...	0.47	-	cyt	0					366
Q8C6Z1 UniProt NPD GO	MUC15_MOUSE	Mucin-15 precursor	0.47	-	end	1	Membrane; single-pass type I membrane protein (Potential)				331

You are viewing entries 27051 to 27100 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.