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
Q94FZ9 UniProt NPD GO	PAP1_BRACM	Plastid lipid-associated protein 1, chloroplast precursor	0.24	-	mit	0	Plastid; chloroplast				327
Q62035 UniProt NPD GO	PTAFR_MOUSE	Platelet-activating factor receptor (PAF-R)	0.24	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			341
Q9XSD4 UniProt NPD GO	PTAFR_PIG	Platelet-activating factor receptor (PAF-R) (PAFr)	0.24	-	end	7 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			342
Q9JKF6 UniProt NPD GO	PVRL1_MOUSE	Poliovirus receptor-related protein 1 precursor (Herpes virus entry mediator C) (HveC) (Nectin-1) (C ...	0.24	-	end	2 *	Membrane; single-pass type I membrane protein	cell-cell adherens junction [IDA]			515
Q5E9A3 UniProt NPD GO	PCBP1_BOVIN	Poly(rC)-binding protein 1	0.24	-	nuc	0	Nucleus. Cytoplasm. Loosely bound in the nucleus. May shuttle between the nucleus and the cytoplasm ...				356
P60335 UniProt NPD GO	PCBP1_MOUSE	Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP-E1)	0.24	-	nuc	0	Nucleus (By similarity)				356
O19048 UniProt NPD GO	PCBP1_RABIT	Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP-E1)	0.24	-	nuc	0	Nucleus (By similarity)				356
Q15365 UniProt NPD GO	PCBP1_HUMAN	Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP-E1) (Nucleic acid-binding protein SUB2.3)	0.24	-	nuc	0	Nucleus. Cytoplasm. Loosely bound in the nucleus. May shuttle between the nucleus and the cytoplasm	cytoplasm [NAS] nucleus [NAS]	601209	1WVN	356
O14327 UniProt NPD GO	PAB2_SCHPO	Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (Poly(A)-binding protein II) (PABII)	0.24	+	nuc	0	Nucleus (By similarity)				166
Q24338 UniProt NPD GO	ESC_DROME	Polycomb protein esc (Protein extra sex combs)	0.24	-	nuc	0	Nucleus	ESC/E(Z) complex [IDA] nuclear chromatin [ISS] nucleus [IDA]			425
P35334 UniProt NPD GO	PGIP1_PHAVU	Polygalacturonase inhibitor 1 precursor (Polygalacturonase-inhibiting protein) (PGIP-1)	0.24	-	exc	0	Cell wall; peripheral membrane protein				342
Q10472 UniProt NPD GO	GALT1_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.24	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Secreted p ...		602273		559
Q8CF93 UniProt NPD GO	GLT13_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 13 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.24	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				556
P83243 UniProt NPD GO	KA131_TITCA	Potassium channel toxin alpha-KTx 13.1 (Toxin Tc1)	0.24	-	nuc	0	Secreted protein	extracellular region [IDA]		1JLZ	23
Q9LD18 UniProt NPD GO	POT4_ARATH	Potassium transporter 4 (AtPOT4) (AtKUP3) (AtKT4)	0.24	-	end	12 *	Cell membrane; multi-pass membrane protein (Potential)				789
P59053 UniProt NPD GO	KCNG3_MOUSE	Potassium voltage-gated channel subfamily G member 3 (Voltage-gated potassium channel subunit Kv6.3) ...	0.24	+	end	7	Cell membrane; multi-pass membrane protein. Has to be associated with KCNB1 or possibly another part ...				433
Q750K9 UniProt NPD GO	SLT11_ASHGO	Pre-mRNA-splicing factor SLT11	0.24	-	cyt	0	Nucleus (By similarity)				331
Q6CAR6 UniProt NPD GO	SYF1_YARLI	Pre-mRNA-splicing factor SYF1	0.24	-	cyt	0	Nucleus (By similarity)				736
Q9XQU4 UniProt NPD GO	SECY_PEA	Preprotein translocase secY subunit, chloroplast precursor (CpSecY)	0.24	-	end	7	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				527
Q8IY26 UniProt NPD GO	PPAC2_HUMAN	Presqualene diphosphate phosphatase (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 domain-contai ...	0.24	-	end	3	Membrane; multi-pass membrane protein (Potential)				295
Q10335 UniProt NPD GO	RPN7_SCHPO	Probable 26S proteasome regulatory subunit rpn7	0.24	-	mit	0					409
Q21217 UniProt NPD GO	GABT_CAEEL	Probable 4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-meth ...	0.24	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				483
O14337 UniProt NPD GO	RM07_SCHPO	Probable 60S ribosomal protein L7, mitochondrial precursor	0.24	-	mit	0					287
Q9H5Z1 UniProt NPD GO	DHX35_HUMAN	Probable ATP-dependent RNA helicase DHX35 (EC 3.6.1.-) (DEAH box protein 35)	0.24	-	cyt	0					703
Q02856 UniProt NPD GO	ABCX_ANTSP	Probable ATP-dependent transporter ycf16	0.24	-	nuc	0	Plastid; chloroplast				251
Q9IA79 UniProt NPD GO	BI1_PAROL	Probable Bax inhibitor 1 (BI-1)	0.24	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				237
Q18359 UniProt NPD GO	NDUA5_CAEEL	Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (EC 1.6.5.3) (EC 1.6.99.3) (NA ...	0.24	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				150
Q8N6M5 UniProt NPD GO	ALLC_HUMAN	Probable allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.24	-	cyt	0					410
O94567 UniProt NPD GO	SYNC_SCHPO	Probable asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS)	0.24	-	cyt	0	Cytoplasm (By similarity)				568
P39986 UniProt NPD GO	ATC6_YEAST	Probable cation-transporting ATPase 1 (EC 3.6.3.-)	0.24	-	end	10 *	Membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] mitochondrion [IDA]			1215
Q9VE00 UniProt NPD GO	C12A4_DROME	Probable cytochrome P450 12a4, mitochondrial precursor (EC 1.14.-.-) (CYPXIIA4)	0.24	-	mit	0	Mitochondrion (Potential)				536
Q9VGZ0 UniProt NPD GO	C12E1_DROME	Probable cytochrome P450 12e1, mitochondrial precursor (EC 1.14.-.-) (CYPXIIE1)	0.24	-	nuc	0	Mitochondrion (Potential)				514
Q08225 UniProt NPD GO	DPP3_YEAST	Probable dipeptidyl-peptidase 3 (EC 3.4.14.4) (Dipeptidyl-peptidase III) (DPP III) (Dipeptidyl amino ...	0.24	-	cyt	0	Cytoplasm (Probable)	cytoplasm [IDA] nucleus [IDA]			711
Q8W474 UniProt NPD GO	DRL7_ARATH	Probable disease resistance protein At1g58390	0.24	-	cyt	0					613
Q9LZ25 UniProt NPD GO	DRL30_ARATH	Probable disease resistance protein At5g04720	0.24	-	cyt	0					811
Q9LNE4 UniProt NPD GO	SCRK3_ARATH	Probable fructokinase-3 (EC 2.7.1.4)	0.24	-	cyt	0					345
Q9FK51 UniProt NPD GO	GALT_ARATH	Probable galactose-1-phosphate uridyl transferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-g ...	0.24	-	nuc	0				1ZWJ	351
Q9Y105 UniProt NPD GO	SYQ_DROME	Probable glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.24	-	cyt	0					778
Q20772 UniProt NPD GO	GCDH_CAEEL	Probable glutaryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.7) (GCD)	0.24	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				409
Q94F49 UniProt NPD GO	H2A5_ARATH	Probable histone H2A.5 (HTA7)	0.24	-	nuc	0	Nucleus (By similarity)				150
Q654M1 UniProt NPD GO	GH37_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.7 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.24	-	cyt	0					620
Q6P0E8 UniProt NPD GO	PPAC3_BRARE	Probable lipid phosphate phosphatase PPAPDC3 (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 doma ...	0.24	-	end	2	Membrane; multi-pass membrane protein (Potential)				287
P38131 UniProt NPD GO	KTR4_YEAST	Probable mannosyltransferase KTR4 (EC 2.4.1.131)	0.24	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				464
Q9VSA3 UniProt NPD GO	ACADM_DROME	Probable medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.24	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial matrix [ISS]			419
O60180 UniProt NPD GO	ARX1_SCHPO	Probable metalloprotease arx1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.24	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				417
Q9M8D3 UniProt NPD GO	PUR4_ARATH	Probable phosphoribosylformylglycinamidine synthase, chloroplast precursor (EC 6.3.5.3) (FGAM syntha ...	0.24	-	mit	0	Plastid; chloroplast (Probable)				1387
Q942X8 UniProt NPD GO	HAK2_ORYSA	Probable potassium transporter 2 (OsHAK2)	0.24	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)				783
Q8TAA1 UniProt NPD GO	RNS11_HUMAN	Probable ribonuclease 11 precursor (EC 3.1.27.-) (RNase 11)	0.24	-	nuc	0	Secreted protein (Potential)				199
O42661 UniProt NPD GO	SMD1_SCHPO	Probable small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1)	0.24	+	nuc	0	Nucleus (By similarity)				117
Q5AXV1 UniProt NPD GO	MCH1_EMENI	Probable transporter mch1	0.24	+	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				615

You are viewing entries 46651 to 46700 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.