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
P34221 UniProt NPD GO	PP2C3_YEAST	Protein phosphatase 2C homolog 3 (EC 3.1.3.16) (PP2C-3)	0.47	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			468
Q24524 UniProt NPD GO	SING_DROME	Protein singed	0.47	-	cyt	0					512
P08953 UniProt NPD GO	TOLL_DROME	Protein toll precursor	0.47	-	end	1	Cell membrane; single-pass type I membrane protein				1097
P28791 UniProt NPD GO	SEC20_YEAST	Protein transport protein SEC20	0.47	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [TAS]			383
Q6C880 UniProt NPD GO	SEC22_YARLI	Protein transport protein SEC22	0.47	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				213
P53992 UniProt NPD GO	SC24C_HUMAN	Protein transport protein Sec24C (SEC24-related protein C)	0.47	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region	COPII vesicle coat [NAS]	607185		1094
Q63645 UniProt NPD GO	PAR2_RAT	Proteinase-activated receptor 2 precursor (PAR-2) (Thrombin receptor-like 1) (Coagulation factor II ...	0.47	-	end	7 *	Membrane; multi-pass membrane protein				397
Q8BIV7 UniProt NPD GO	S45A1_MOUSE	Proton-associated sugar transporter A (PAST-A) (Solute carrier family 45 member 1) (Deleted in neuro ...	0.47	-	end	11	Membrane; multi-pass membrane protein (Potential)				751
P22311 UniProt NPD GO	PU91_SCICO	Puff II/9-1 protein precursor	0.47	-	exc	0					286
Q92359 UniProt NPD GO	YDHE_SCHPO	Pumilio domain-containing protein C6G9.14	0.47	-	nuc	0					681
Q6AXX9 UniProt NPD GO	ABEC4_RAT	Putative C->U-editing enzyme APOBEC-4 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme catalytic p ...	0.47	-	nuc	0					388
Q6B8L8 UniProt NPD GO	RPOZ_GRATL	Putative DNA-directed RNA polymerase omega chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase ...	0.47	-	nuc	0	Plastid; chloroplast				80
P49518 UniProt NPD GO	YCF30_ODOSI	Putative HTH-type transcriptional regulator ycf30	0.47	-	cyt	0	Plastid; chloroplast				309
Q9THX6 UniProt NPD GO	TL29_LYCES	Putative L-ascorbate peroxidase, chloroplast precursor (EC 1.11.1.11) (Thylakoid lumenal 29 kDa prot ...	0.47	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				345
Q09299 UniProt NPD GO	YQOA_CAEEL	Putative RNA-binding protein EEED8.10	0.47	-	nuc	0					738
P49583 UniProt NPD GO	PCY1_CAEEL	Putative choline-phosphate cytidylyltransferase (EC 2.7.7.15) (Phosphorylcholine transferase) (CTP:p ...	0.47	-	nuc	0					362
Q9VKH0 UniProt NPD GO	COG8_DROME	Putative conserved oligomeric Golgi complex component 8	0.47	-	cyt	0	Golgi apparatus (By similarity)				570
Q9LVT3 UniProt NPD GO	DRL38_ARATH	Putative disease resistance protein At5g47260	0.47	-	cyt	0					885
Q9P327 UniProt NPD GO	PLB4_SCHPO	Putative lysophospholipase C977.09c/C1348.10c precursor (EC 3.1.1.5) (Phospholipase B)	0.47	-	cyt	0	Secreted protein (Probable)				673
Q6YPG5 UniProt NPD GO	NOS_ORYSA	Putative nitric-oxide synthase (EC 1.14.13.39)	0.47	+	mit	0					547
Q9SVQ6 UniProt NPD GO	PEL14_ARATH	Putative pectate lyase 14 precursor (EC 4.2.2.2)	0.47	-	exc	1 *					418
Q9C691 UniProt NPD GO	DEGP6_ARATH	Putative protease Do-like 6, chloroplast precursor (EC 3.4.21.-)	0.47	+	mit	0	Plastid; chloroplast (Potential)				257
Q9H0A9 UniProt NPD GO	CU056_HUMAN	Putative protein C21orf56	0.47	-	nuc	0					340
P43298 UniProt NPD GO	TMK1_ARATH	Putative receptor protein kinase TMK1 precursor (EC 2.7.11.1)	0.47	-	end	1	Membrane; single-pass type I membrane protein				942
Q9VX10 UniProt NPD GO	SRX_DROME	Putative sulfiredoxin (EC 1.8.98.2)	0.47	-	nuc	0					162
Q9FJ16 UniProt NPD GO	APRR4_ARATH	Putative two-component response regulator-like APRR4 (Pseudo-response regulator 4)	0.47	-	cyt	0	Nucleus (Probable)				292
P47157 UniProt NPD GO	YJ90_YEAST	Putative uncharacterized protein YJR120W precursor	0.47	-	nuc	0					116
Q9SRQ8 UniProt NPD GO	ATL3A_ARATH	RING-H2 finger protein ATL3A	0.47	-	nuc	1					356
Q08237 UniProt NPD GO	REXO4_YEAST	RNA exonuclease 4 (EC 3.1.-.-)	0.47	+	nuc	0	Nucleus	nucleolus [IDA] nucleus [IDA]			289
Q10110 UniProt NPD GO	RRN3_SCHPO	RNA polymerase I-specific transcription initiation factor rrn3	0.47	-	cyt	0	Nucleus (By similarity)	RNA polymerase I transcription factor complex [IC]			599
Q6FWA7 UniProt NPD GO	TFB4_CANGA	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.47	-	nuc	0	Nucleus (By similarity)				335
P24386 UniProt NPD GO	RAE1_HUMAN	Rab proteins geranylgeranyltransferase component A 1 (Rab escort protein 1) (REP-1) (Choroideraemia ...	0.47	-	nuc	0		Rab-protein geranylgeranyltransferase complex [TAS]	303100		653
P50749 UniProt NPD GO	RASF2_HUMAN	Ras association domain-containing protein 2	0.47	-	nuc	0	Nucleus		609492		326
Q8BMS9 UniProt NPD GO	RASF2_MOUSE	Ras association domain-containing protein 2	0.47	-	nuc	0					326
Q3B7D5 UniProt NPD GO	RASF2_RAT	Ras association domain-containing protein 2	0.47	-	nuc	0					326
P21860 UniProt NPD GO	ERBB3_HUMAN	Receptor tyrosine-protein kinase erbB-3 precursor (EC 2.7.10.1) (c-erbB3) (Tyrosine kinase-type cell ...	0.47	+	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS]	190151	1M6B	1342
O08617 UniProt NPD GO	PTPRR_RAT	Receptor-type tyrosine-protein phosphatase R precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase P ...	0.47	-	end	1	Isoform 4: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 1, isoform 2, ...	cell surface [ISS]			656
Q9BYZ8 UniProt NPD GO	REG4_HUMAN	Regenerating islet-derived protein 4 precursor (Reg IV) (REG-like protein) (Gastrointestinal secreto ...	0.47	-	exc	0	Secreted protein		609846		158
Q92900 UniProt NPD GO	RENT1_HUMAN	Regulator of nonsense transcripts 1 (EC 3.6.1.-) (ATP-dependent helicase RENT1) (Nonsense mRNA reduc ...	0.47	-	nuc	0	Cytoplasm	chromatin [IDA] cytoplasm [NAS]	601430		1129
O94697 UniProt NPD GO	RFC5_SCHPO	Replication factor C subunit 5 (Replication factor C5)	0.47	-	nuc	0	Nucleus (By similarity)	Ctf18 RFC-like complex [TAS] Elg1 RFC-like complex [IDA] Rad17 RFC-like complex [TAS]			358
Q7M6Z0 UniProt NPD GO	R4RL2_MOUSE	Reticulon-4 receptor-like 2 precursor (Nogo-66 receptor homolog 1) (Nogo-66 receptor-related protein ...	0.47	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	anchored to plasma membrane [ISS]			420
P28700 UniProt NPD GO	RXRA_MOUSE	Retinoic acid receptor RXR-alpha (Retinoid X receptor alpha)	0.47	+	nuc	0	Nucleus			1XDK	467
Q9DD06 UniProt NPD GO	TIG2_MOUSE	Retinoic acid receptor responder protein 2 precursor	0.47	-	vac	0	Secreted protein (Potential)				162
Q9UST8 UniProt NPD GO	RNH1_SCHPO	Ribonuclease H (EC 3.1.26.4) (RNase H)	0.47	-	nuc	0					264
Q40875 UniProt NPD GO	RNS3_PETHY	Ribonuclease S-3 precursor (EC 3.1.27.1) (Stylar glycoprotein 3) (S3-RNase)	0.47	-	exc	0	Secreted protein; extracellular space				222
Q75BW5 UniProt NPD GO	RNY1_ASHGO	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.47	-	exc	1 *	Secreted protein (By similarity)				292
Q9Z1M4 UniProt NPD GO	KS6B2_MOUSE	Ribosomal protein S6 kinase beta-2 (EC 2.7.11.1) (S6K-beta 2) (70 kDa ribosomal protein S6 kinase 2) ...	0.47	-	cyt	0					485
Q9HGL6 UniProt NPD GO	BRX1_SCHPO	Ribosome biogenesis protein Brix homolog	0.47	-	nuc	0	Nucleus; nucleolus (By similarity)				295
Q4P6N7 UniProt NPD GO	RUVB2_USTMA	RuvB-like helicase 2 (EC 3.6.1.-)	0.47	-	cyt	0	Nucleus (By similarity)				476
Q8IYR2 UniProt NPD GO	SMYD4_HUMAN	SET and MYND domain-containing protein 4	0.47	-	nuc	0					804

You are viewing entries 27201 to 27250 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.