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
Q9R193 UniProt NPD GO	AT1B4_RAT	X/potassium-transporting ATPase subunit beta-m (X,K-ATPase beta-m subunit)	0.31	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				356
P23507 UniProt NPD GO	XA1_XENLA	XA-1 protein precursor	0.31	-	nuc	0					198
Q5GH57 UniProt NPD GO	XKR6_RAT	XK-related protein 6	0.31	-	end	6	Membrane; multi-pass membrane protein (Potential)				638
P08793 UniProt NPD GO	XDH_CALVI	Xanthine dehydrogenase (EC 1.17.1.4) (XD)	0.31	-	cyt	0	Peroxisome				1353
P06678 UniProt NPD GO	ZEAA_MAIZE	Zein-alpha 19D1 precursor (19 kDa zein 19D1)	0.31	-	exc	1 *					240
P04700 UniProt NPD GO	ZEAX_MAIZE	Zein-alpha PZ22.1/22A1 precursor (22 kDa zein PZ22.1/22A1)	0.31	-	exc	1 *					263
P04699 UniProt NPD GO	ZEAY_MAIZE	Zein-alpha ZA1/M1 precursor (22 kDa zein ZA1/M1)	0.31	-	exc	1 *					266
P06673 UniProt NPD GO	ZEB1_MAIZE	Zein-beta precursor (16 kDa) (Zein 2) (Clone 15A3)	0.31	-	exc	0	Protein body. Endosperm protein bodies				180
Q8BX51 UniProt NPD GO	SGCZ_MOUSE	Zeta-sarcoglycan (Zeta-SG) (ZSG1)	0.31	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)	plasma membrane [IDA] sarcoglycan complex [IDA]			311
Q6UIM1 UniProt NPD GO	ZNHI3_MACMU	Zinc finger HIT domain-containing protein 3 (Thyroid receptor-interacting protein 3) (TRIP-3) (Thyro ...	0.31	-	nuc	0					147
P35275 UniProt NPD GO	ZN126_HUMAN	Zinc finger protein 126 (HZF-2) (Fragment)	0.31	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194633		98
Q96NJ3 UniProt NPD GO	ZN285_HUMAN	Zinc finger protein 285	0.31	-	nuc	0	Nucleus (Probable)				435
Q6J1I8 UniProt NPD GO	ZN313_PIG	Zinc finger protein 313	0.31	-	nuc	0					228
Q8N9K5 UniProt NPD GO	ZN565_HUMAN	Zinc finger protein 565	0.31	-	nuc	0	Nucleus (Potential)				499
Q91VY9 UniProt NPD GO	ZN622_MOUSE	Zinc finger protein 622	0.31	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				476
Q9H7S9 UniProt NPD GO	ZN703_HUMAN	Zinc finger protein 703	0.31	-	nuc	0					590
P51507 UniProt NPD GO	ZNF80_PONPY	Zinc finger protein 80	0.31	-	nuc	0	Nucleus (Probable)				273
P55115 UniProt NPD GO	NAS15_CAEEL	Zinc metalloproteinase nas-15 precursor (EC 3.4.24.21) (Nematode astacin 15)	0.31	-	exc	0	Secreted protein (Potential)				571
Q12836 UniProt NPD GO	ZP4_HUMAN	Zona pellucida sperm-binding protein 4 precursor (Zona pellucida sperm-binding protein B)	0.31	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				540
O14874 UniProt NPD GO	BCKD_HUMAN	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.4) (B ...	0.31	-	nuc	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [TAS] mitochondrion [TAS]			412
O88345 UniProt NPD GO	PDK4_SPETR	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.31	-	mit	0	Mitochondrion; mitochondrial matrix				412
Q9P2J9 UniProt NPD GO	PDP2_HUMAN	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 2, mitochondrial precursor (EC 3.1.3.43) (PDP 2) (P ...	0.31	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				529
P06244 UniProt NPD GO	KAPA_YEAST	cAMP-dependent protein kinase type 1 (EC 2.7.11.11) (PKA 1) (CDC25-suppressing protein kinase) (PK-2 ...	0.31	-	cyt	0		cAMP-dependent protein kinase complex [IMP] cytoplasm [TAS]		1FOT	397
P33201 UniProt NPD GO	MRT4_YEAST	mRNA turnover protein 4	0.31	-	mit	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			236
Q6FJ04 UniProt NPD GO	MRT4_CANGA	mRNA turnover protein 4 homolog	0.31	-	mit	0	Nucleus; nucleolus (By similarity)				239
Q1LWG4 UniProt NPD GO	PCAT1_BRARE	1-acylglycerophosphocholine O-acyltransferase 1 (EC 2.3.1.23) (Lung-type acyl-coa:lysophosphatidylch ...	0.30	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...				517
P42704 UniProt NPD GO	LPPRC_HUMAN	130 kDa leucine-rich protein (LRP 130) (GP130) (Leucine-rich PPR motif-containing protein)	0.30	-	nuc	0		cytoplasm [ISS] mitochondrion [IDA] nucleus [IDA]	607544		1273
Q9CQV8 UniProt NPD GO	1433B_MOUSE	14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1) (KCIP-1)	0.30	-	nuc	0	Cytoplasm (By similarity)				245
Q6PC29 UniProt NPD GO	1433G_BRARE	14-3-3 protein gamma	0.30	-	nuc	0	Cytoplasm (By similarity)				247
Q5F3W6 UniProt NPD GO	1433G_CHICK	14-3-3 protein gamma	0.30	-	nuc	0	Cytoplasm (By similarity)				247
Q6PCG0 UniProt NPD GO	143GA_XENLA	14-3-3 protein gamma-A	0.30	-	nuc	0	Cytoplasm (By similarity)				247
O49995 UniProt NPD GO	1433B_TOBAC	14-3-3-like protein B	0.30	-	nuc	0					255
Q7XTE8 UniProt NPD GO	14332_ORYSA	14-3-3-like protein GF14-B (G-box factor 14-3-3 homolog B)	0.30	-	nuc	0	Cytoplasm. Nucleus				262
O15528 UniProt NPD GO	CP27B_HUMAN	25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial precursor (EC 1.14.13.13) (Cytochrome P450 su ...	0.30	-	mit	0	Mitochondrion		609506		508
P62333 UniProt NPD GO	PRS10_HUMAN	26S protease regulatory subunit S10B (Proteasome subunit p42) (Proteasome 26S subunit ATPase 6)	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA] proteasome complex (sensu Eukaryota) [IDA]	602708		389
P62334 UniProt NPD GO	PRS10_MOUSE	26S protease regulatory subunit S10B (Proteasome subunit p42) (Proteasome 26S subunit ATPase 6)	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				389
P62335 UniProt NPD GO	PRS10_SPETR	26S protease regulatory subunit S10B (Proteasome subunit p42) (Proteasome 26S subunit ATPase 6) (Con ...	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				389
P18250 UniProt NPD GO	LEU2_PHYBL	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.30	-	mit	0					744
Q5XIE3 UniProt NPD GO	RM11_RAT	39S ribosomal protein L11, mitochondrial precursor (L11mt) (MRP-L11)	0.30	-	nuc	0	Mitochondrion (By similarity)				203
Q9D1B9 UniProt NPD GO	RM28_MOUSE	39S ribosomal protein L28, mitochondrial precursor (L28mt) (MRP-L28)	0.30	-	mit	0	Mitochondrion				257
P49393 UniProt NPD GO	RS13_XENLA	40S ribosomal protein S13	0.30	-	nuc	0					150
Q9FML6 UniProt NPD GO	RS15F_ARATH	40S ribosomal protein S15-6	0.30	-	cyt	0	Cytoplasm				160
Q9SQZ1 UniProt NPD GO	RS17C_ARATH	40S ribosomal protein S17-3	0.30	-	nuc	0					139
Q8JGS9 UniProt NPD GO	RS18_BRARE	40S ribosomal protein S18	0.30	-	mit	0	Cytoplasm				152
Q7KS38 UniProt NPD GO	RS19B_DROME	40S ribosomal protein S19b	0.30	-	nuc	0					154
Q4R5H5 UniProt NPD GO	RS24_MACFA	40S ribosomal protein S24	0.30	-	nuc	0					131
P14249 UniProt NPD GO	RS24_RHIRA	40S ribosomal protein S24	0.30	+	nuc	0					148
P62276 UniProt NPD GO	RS29_BOVIN	40S ribosomal protein S29	0.30	-	mit	0					55
P62273 UniProt NPD GO	RS29_HUMAN	40S ribosomal protein S29	0.30	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603633		55
P62274 UniProt NPD GO	RS29_MOUSE	40S ribosomal protein S29	0.30	-	mit	0					55

You are viewing entries 40001 to 40050 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.