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
Q9FLV5 UniProt NPD GO	PER61_ARATH	Probable peroxidase 61 precursor (EC 1.11.1.7) (Atperox P61)	0.07	-	mit	0	Secreted protein (By similarity)				340
P94063 UniProt NPD GO	HAL3B_ARATH	Probable phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) (Halotolerance protein Hal3b) (AtHa ...	0.07	-	cyt	0					201
Q2N2K0 UniProt NPD GO	PHYK3_SOYBN	Probable phytol kinase 3, chloroplast precursor (EC 2.7.-.-)	0.07	-	end	6	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				319
Q9TLZ0 UniProt NPD GO	RRP3_CYACA	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.07	-	cyt	0	Plastid; chloroplast				101
Q9BAB9 UniProt NPD GO	RRP3_EUGVI	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.07	-	mit	0	Plastid; chloroplast				101
Q7XLC6 UniProt NPD GO	HAK11_ORYSA	Probable potassium transporter 11 (OsHAK11)	0.07	-	end	13 *	Membrane; multi-pass membrane protein (By similarity)				791
Q9SRG3 UniProt NPD GO	PDI2_ARATH	Probable protein disulfide-isomerase 2 precursor (EC 5.3.4.1) (PDI 2)	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				508
Q9ZNR6 UniProt NPD GO	PDXL2_ARATH	Probable pyridoxin biosynthesis PDX1-like protein 2	0.07	-	cyt	0		cytosol [IDA]			314
P55869 UniProt NPD GO	XAG2_XENLA	Probable secreted protein XAG-2 precursor (Secreted protein np77)	0.07	-	exc	0	Secreted protein (Probable)				185
O44953 UniProt NPD GO	SPCS1_CAEEL	Probable signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				105
P58684 UniProt NPD GO	SPCS2_ARATH	Probable signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				192
Q9XTU6 UniProt NPD GO	RUXE_CAEEL	Probable small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.07	-	mit	0	Nucleus (By similarity)				90
Q18786 UniProt NPD GO	SMD2_CAEEL	Probable small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.07	-	nuc	0	Nucleus (By similarity)				118
Q9UTJ7 UniProt NPD GO	DHSA_SCHPO	Probable succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3. ...	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				641
Q94FY8 UniProt NPD GO	TOCC_MAIZE	Probable tocopherol cyclase, chloroplast precursor (Sucrose export defective 1)	0.07	-	mit	0	Plastid; chloroplast				474
Q9NEX2 UniProt NPD GO	T2AG_CAEEL	Probable transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TF ...	0.07	-	cyt	0	Nucleus (By similarity)				113
Q4IM48 UniProt NPD GO	MCH1_GIBZE	Probable transporter MCH1	0.07	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				572
P34477 UniProt NPD GO	UBC7_CAEEL	Probable ubiquitin-conjugating enzyme E2 7 (EC 6.3.2.19) (Ubiquitin-protein ligase 7) (Ubiquitin car ...	0.07	-	nuc	0				1PZV	164
Q12063 UniProt NPD GO	UPPS_YEAST	Probable undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) (UPP synthetase) (Di-trans,poly-cis-dec ...	0.07	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential). Lip ...	endoplasmic reticulum [IDA] lipid particle [IDA] nuclear envelope [IDA]			375
O74409 UniProt NPD GO	URIC_SCHPO	Probable uricase (EC 1.7.3.3) (Urate oxidase)	0.07	-	cyt	0					296
Q41542 UniProt NPD GO	XTH_WHEAT	Probable xyloglucan endotransglucosylase/hydrolase precursor (EC 2.4.1.207)	0.07	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				293
Q8W246 UniProt NPD GO	ZIP7_ARATH	Probable zinc transporter 7 precursor (ZRT/IRT-like protein 7)	0.07	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				365
Q8R4W6 UniProt NPD GO	PCOC2_MOUSE	Procollagen C-endopeptidase enhancer 2 precursor (Procollagen COOH-terminal proteinase enhancer 2) ( ...	0.07	-	end	0	Secreted protein (Probable)				414
O42471 UniProt NPD GO	GON2B_CARAU	Progonadoliberin IIB precursor [Contains: Gonadoliberin II (Luteinizing hormone-releasing hormone II ...	0.07	-	exc	1 *	Secreted protein				86
P70074 UniProt NPD GO	GON1_PAGMA	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.07	-	exc	0	Secreted protein				95
P13684 UniProt NPD GO	LEVI_XENLA	Prolevitide precursor [Contains: Amphipathic peptide; Levitide]	0.07	-	exc	0	Secreted protein				88
P26228 UniProt NPD GO	SBPI_SARBU	Protease inhibitor (SBPI)	0.07	-	nuc	0					57
P40302 UniProt NPD GO	PSA1_YEAST	Proteasome component PRE5 (EC 3.4.25.1) (Macropain subunit PRE5) (Proteinase YSCE subunit PRE5) (Mul ...	0.07	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, alpha-subunit comp... [IPI]		2FNY	234
P32379 UniProt NPD GO	PSA5_YEAST	Proteasome component PUP2 (EC 3.4.25.1) (Macropain subunit PUP2) (Proteinase YSCE subunit PUP2) (Mul ...	0.07	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, alpha-subunit comp... [IPI]		2FNY	260
O23708 UniProt NPD GO	PSA2A_ARATH	Proteasome subunit alpha type 2-A (EC 3.4.25.1) (20S proteasome alpha subunit B) (Proteasome compone ...	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				235
Q8L4A7 UniProt NPD GO	PSA2B_ARATH	Proteasome subunit alpha type 2-B (EC 3.4.25.1) (20S proteasome alpha subunit B-2)	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				235
P18053 UniProt NPD GO	PSA4_DROME	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome 29 kDa subunit) (PROS-Dm29)	0.07	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				264
O14818 UniProt NPD GO	PSA7_HUMAN	Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome subunit RC6-1) (Proteasome subunit XAPC7)	0.07	-	mit	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	606607		248
P28024 UniProt NPD GO	PSB4_XENLA	Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome beta chain) (Macropain beta chain ...	0.07	-	cyt	0	Cytoplasm. Nucleus				242
Q7DLR9 UniProt NPD GO	PSB4_ARATH	Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome subunit beta type 7) (20S proteas ...	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
P20658 UniProt NPD GO	PR10_CAVPO	Protein 10 (29 kDa brain-specific calcium-binding protein) (Fragments)	0.07	-	cyt	0					92
Q9UHM2 UniProt NPD GO	AD13_HUMAN	Protein AD-013	0.07	-	end	1 *					190
Q755P0 UniProt NPD GO	AF9_ASHGO	Protein AF-9 homolog	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				208
P53930 UniProt NPD GO	AF9_YEAST	Protein AF-9 homolog	0.07	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] H4/H2A histone acetyltransferase complex [IPI] nucleus [IDA] SWR1 complex [IPI]			226
O22969 UniProt NPD GO	Y2416_ARATH	Protein At2g34160	0.07	-	cyt	0				1VM0	130
Q9LEV3 UniProt NPD GO	UMP3_ARATH	Protein At5g10860, mitochondrial precursor	0.07	-	mit	0	Mitochondrion				206
Q9DCV5 UniProt NPD GO	CJ057_MOUSE	Protein C10orf57 homolog	0.07	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				123
Q6DCU7 UniProt NPD GO	CK073_XENLA	Protein C11orf73 homolog	0.07	-	cyt	0	Cytoplasm (By similarity)				197
Q9H867 UniProt NPD GO	CN138_HUMAN	Protein C14orf138	0.07	-	cyt	0					144
Q96F85 UniProt NPD GO	CB032_HUMAN	Protein C2orf32	0.07	-	cyt	0					164
Q9H1X1 UniProt NPD GO	CF206_HUMAN	Protein C6orf206	0.07	-	mit	0					276
Q9P0K9 UniProt NPD GO	CI004_HUMAN	Protein C9orf4 (Brain protein CG-6)	0.07	-	end	1	Membrane; single-pass membrane protein (Potential)		604574		344
P53198 UniProt NPD GO	ERP6_YEAST	Protein ERP6 precursor	0.07	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	mitochondrion [IDA]			216
Q7SYC7 UniProt NPD GO	FA11L_BRARE	Protein FAM11-like	0.07	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				351
Q5R9I4 UniProt NPD GO	FA18B_PONPY	Protein FAM18B	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				205

You are viewing entries 70801 to 70850 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.