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
Q9EQQ4 UniProt NPD GO	GPR45_MOUSE	Probable G-protein coupled receptor 45 (PSP24-alpha) (PSP24-1)	0.21	-	vac	7 *	Membrane; multi-pass membrane protein				373
Q69SV0 UniProt NPD GO	APX8_ORYSA	Probable L-ascorbate peroxidase 8, chloroplast precursor (EC 1.11.1.11)	0.21	-	nuc	1	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				478
Q19724 UniProt NPD GO	NUMM_CAEEL	Probable NADH-ubiquinone oxidoreductase 13 kDa-A subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1 ...	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				140
Q9USN3 UniProt NPD GO	UTP13_SCHPO	Probable U3 small nucleolar RNA-associated protein 13 (U3 snoRNA-associated protein 13)	0.21	-	cyt	0	Nucleus; nucleolus (By similarity)				777
Q27906 UniProt NPD GO	ABP2_RIPCL	Probable antibacterial peptide precursor	0.21	-	exc	1 *	Secreted protein (Potential)				150
Q27535 UniProt NPD GO	KARG2_CAEEL	Probable arginine kinase ZC434.8 (EC 2.7.3.3) (AK)	0.21	-	cyt	0					360
Q9SKJ5 UniProt NPD GO	CESAA_ARATH	Probable cellulose synthase A catalytic subunit 10 [UDP-forming] (EC 2.4.1.12) (AtCesA-10) (AtCesA-1 ...	0.21	-	end	8	Cell membrane; multi-pass membrane protein (Probable)				1065
P53703 UniProt NPD GO	CCHL_CAEEL	Probable cytochrome c-type heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome-c-type synthase)	0.21	+	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				280
Q09363 UniProt NPD GO	SQV8_CAEEL	Probable glucuronosyltransferase sqv-8 (EC 2.4.1.135) (Vulval invagination protein sqv-8) (Squashed ...	0.21	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				356
Q9SZ11 UniProt NPD GO	GLPQ2_ARATH	Probable glycerophosphoryl diester phosphodiesterase 2 precursor (EC 3.1.4.46)	0.21	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				759
Q9U2D9 UniProt NPD GO	GYS_CAEEL	Probable glycogen [starch] synthase (EC 2.4.1.11)	0.21	-	cyt	0					672
Q10265 UniProt NPD GO	HSP71_SCHPO	Probable heat shock protein ssa1	0.21	-	cyt	0	Cytoplasm (Potential)				643
O77392 UniProt NPD GO	IPYR_PLAF7	Probable inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.21	-	nuc	0					380
Q9DCG6 UniProt NPD GO	MAWB2_MOUSE	Probable isomerase MAWBP-2 (EC 5.1.-.-)	0.21	-	cyt	0					288
Q9VYI3 UniProt NPD GO	RM49_DROME	Probable mitochondrial 39S ribosomal protein L49 (L49mt)	0.21	-	mit	0	Mitochondrion (By similarity)				179
Q9C0W1 UniProt NPD GO	NRK1_SCHPO	Probable nicotinamide riboside kinase 1 (EC 2.7.1.-)	0.21	-	nuc	0					230
Q68FT3 UniProt NPD GO	CJ033_RAT	Probable oxidoreductase C10orf33 homolog (EC 1.-.-.-)	0.21	-	mit	0					581
O22862 UniProt NPD GO	PER26_ARATH	Probable peroxidase 26 precursor (EC 1.11.1.7) (Atperox P26) (ATP50)	0.21	-	nuc	0	Secreted protein (By similarity)				335
O74382 UniProt NPD GO	SERB_SCHPO	Probable phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase)	0.21	-	cyt	0					298
O80760 UniProt NPD GO	Y639_ARATH	Probable polygalacturonase non-catalytic subunit At1g60390 precursor (Aromatic-rich glycoprotein At1 ...	0.21	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity). Cell wall (By similarity). Associat ...				624
Q7XIV8 UniProt NPD GO	HAK9_ORYSA	Probable potassium transporter 9 (OsHAK9)	0.21	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				788
Q9D236 UniProt NPD GO	HTRA3_MOUSE	Probable serine protease HTRA3 precursor (EC 3.4.21.-) (High-temperature requirement factor A3) (Pre ...	0.21	-	exc	0	Secreted protein (By similarity)				459
Q9UU87 UniProt NPD GO	KC61_SCHPO	Probable serine/threonine-protein kinase C1919.01 (EC 2.7.11.1)	0.21	-	cyt	0					354
Q12093 UniProt NPD GO	TRMU_YEAST	Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61)	0.21	-	mit	0		mitochondrion [IDA]			417
Q9ZQX4 UniProt NPD GO	VATF_ARATH	Probable vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F ...	0.21	-	cyt	0					128
Q9SJL9 UniProt NPD GO	XTH32_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 32 precursor (EC 2.4.1.207) (At-XTH32) (X ...	0.21	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				299
Q5R9N3 UniProt NPD GO	PLOD1_PONPY	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH ...	0.21	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				727
Q8R416 UniProt NPD GO	PKR1_RAT	Prokineticin receptor 1 (PK-R1) (G-protein coupled receptor 73) (G-protein coupled receptor ZAQ)	0.21	-	end	7	Membrane; multi-pass membrane protein				393
Q8R415 UniProt NPD GO	PKR2_RAT	Prokineticin receptor 2 (PK-R2) (G-protein coupled receptor 73-like 1) (G-protein coupled receptor I ...	0.21	+	end	7	Membrane; multi-pass membrane protein				383
Q9HCU5 UniProt NPD GO	PREB_HUMAN	Prolactin regulatory element-binding protein (Mammalian guanine nucleotide exchange factor mSec12)	0.21	-	cyt	2	Nucleus (By similarity). Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane ...	nucleus [TAS]	606395		417
Q86XR5 UniProt NPD GO	PRIMA_HUMAN	Proline-rich membrane anchor 1 precursor (PRiMA)	0.21	-	exc	1 *	Membrane; single-pass type I membrane protein (By similarity)				153
Q767L1 UniProt NPD GO	PRR3_PIG	Proline-rich protein 3 (MHC class I region proline-rich protein CAT56) (Fragment)	0.21	-	nuc	0					131
P43252 UniProt NPD GO	PI2R_MOUSE	Prostacyclin receptor (Prostanoid IP receptor) (PGI receptor) (Prostaglandin I2 receptor)	0.21	-	end	6 *	Membrane; multi-pass membrane protein				415
Q66LN0 UniProt NPD GO	PGES2_BOVIN	Prostaglandin E synthase 2 (EC 5.3.99.3) (Microsomal prostaglandin E synthase 2) (mPGES-2) [Contains ...	0.21	-	mit	0	Golgi apparatus; Golgi membrane; single-pass membrane protein (Probable). Processed form: Cytoplasm. ...				79
P34979 UniProt NPD GO	PE2R3_BOVIN	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype)	0.21	+	end	6 *	Membrane; multi-pass membrane protein				417
Q64L94 UniProt NPD GO	PSME1_PIG	Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a)	0.21	-	cyt	0					249
Q5W416 UniProt NPD GO	PSB8_CANFA	Proteasome subunit beta type 8 precursor (EC 3.4.25.1)	0.21	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				276
P49934 UniProt NPD GO	PG5_PIG	Protegrin-5 precursor (PG-5)	0.21	-	mit	1 *	Secreted protein				149
Q01217 UniProt NPD GO	ARG56_YEAST	Protein ARG5,6, mitochondrial precursor [Contains: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1 ...	0.21	-	mit	0	Mitochondrion	mitochondrial matrix [IDA]			863
Q8L8Q8 UniProt NPD GO	Y5486_ARATH	Protein At5g64816 precursor	0.21	-	nuc	0					130
Q9FIT4 UniProt NPD GO	BFT_ARATH	Protein BROTHER of FT and TFL1	0.21	-	cyt	0	Cytoplasm (By similarity)				177
Q6PDY2 UniProt NPD GO	CJ022_MOUSE	Protein C10orf22 homolog	0.21	-	mit	0					256
Q5REK7 UniProt NPD GO	CJ032_PONPY	Protein C10orf32 homolog	0.21	-	nuc	0					106
Q8K207 UniProt NPD GO	CA021_MOUSE	Protein C1orf21 homolog	0.21	-	nuc	0					121
Q6PDS0 UniProt NPD GO	CT102_MOUSE	Protein C20orf102 homolog precursor	0.21	-	nuc	0					220
Q96N03 UniProt NPD GO	CT102_HUMAN	Protein C20orf102 precursor	0.21	-	nuc	0					204
Q9P1F3 UniProt NPD GO	CF115_HUMAN	Protein C6orf115	0.21	+	cyt	0					81
Q12421 UniProt NPD GO	CIS1_YEAST	Protein CIS1 (CIK1 suppressor protein 1)	0.21	-	nuc	0	Punctate structures	cytoplasm [IDA]			196
Q13286 UniProt NPD GO	CLN3_HUMAN	Protein CLN3 (Battenin) (Batten disease protein)	0.21	-	end	11 *	Lysosome; lysosomal membrane; multi-pass membrane protein	mitochondrion [TAS]	607042		438
Q8BGC9 UniProt NPD GO	CREG2_MOUSE	Protein CREG2 precursor	0.21	-	mit	0	Secreted protein	endoplasmic reticulum [IDA] Golgi apparatus [IDA]			288

You are viewing entries 49901 to 49950 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.