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
Q07831 UniProt NPD GO	PFPN_ENTHI	Nonpathogenic pore-forming peptide precursor (APNP)	0.00	-	end	0	Cytoplasm				97
P84160 UniProt NPD GO	NLTP_CITLI	Nonspecific lipid-transfer protein (LTP) (Allergen Cit l 3) (Fragment)	0.00	-		0					20
P84161 UniProt NPD GO	NLTP_CITSI	Nonspecific lipid-transfer protein (LTP) (Allergen Cit s 3.0101) (Fragment)	0.00	-		0					20
P0C088 UniProt NPD GO	NLTP_ARTVU	Nonspecific lipid-transfer protein (LTP) (Pollen allergen Art v 3) (Fragment)	0.00	-	nuc	0					37
P39085 UniProt NPD GO	NLTP2_WHEAT	Nonspecific lipid-transfer protein 2 (LTP 2) (W-FABP) (Fragment)	0.00	-	mit	0					28
Q9LLR6 UniProt NPD GO	NLTP4_ARATH	Nonspecific lipid-transfer protein 4 precursor (LTP 4)	0.00	-	exc	1 *					112
P80274 UniProt NPD GO	NLTP4_VITSX	Nonspecific lipid-transfer protein P4 (LTP P4) (Fragment)	0.00	-	nuc	0					37
Q23655 UniProt NPD GO	NLT1_CAEEL	Nonspecific lipid-transfer protein-like	0.00	-	pox	0					118
P83722 UniProt NPD GO	NU160_XENLA	Nuclear pore complex protein Nup160 (Nucleoporin Nup160) (Fragments)	0.00	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex. Cytoplasm				44
Q9CWU9 UniProt NPD GO	NUP37_MOUSE	Nucleoporin Nup37	0.00	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				326
Q8NFH4 UniProt NPD GO	NUP37_HUMAN	Nucleoporin Nup37 (p37)	0.00	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex				326
Q75DD1 UniProt NPD GO	NDK_ASHGO	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0					151
Q7Z8P9 UniProt NPD GO	NDK_ASPFU	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0					153
Q9M7P6 UniProt NPD GO	NDK_CAPAN	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0					148
Q90380 UniProt NPD GO	NDK_COLLI	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0	Cytoplasm. Cell membrane				153
Q9UUY8 UniProt NPD GO	NDK_NEUCR	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0					152
P36010 UniProt NPD GO	NDK_YEAST	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0	Cytoplasm	cytosol [IDA] mitochondrial intermembrane space [IDA]			153
Q8TFN0 UniProt NPD GO	NDK_EMENI	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase) (AnNDK)	0.00	-	cyt	0					153
P27950 UniProt NPD GO	NDK_GINCI	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase) (Fragment)	0.00	-	cyt	0					151
P47921 UniProt NPD GO	NDK_LYCES	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase) (Fragment)	0.00	-	cyt	0					144
Q9UR66 UniProt NPD GO	NDK_CANAL	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase) (NDPK) (Fragment)	0.00	-	cyt	0	Cytoplasm				21
P39207 UniProt NPD GO	NDK1_ARATH	Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I ...	0.00	-	cyt	0				1U8W	149
O81372 UniProt NPD GO	NDK1_MESCR	Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I ...	0.00	-	cyt	0					148
P47922 UniProt NPD GO	NDK1_PEA	Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I ...	0.00	-	cyt	0					149
Q13232 UniProt NPD GO	NDK3_HUMAN	Nucleoside diphosphate kinase 3 (EC 2.7.4.6) (NDK 3) (NDP kinase 3) (Nucleoside diphosphate kinase C ...	0.00	-	nuc	0			601817	1ZS6	169
Q9WV85 UniProt NPD GO	NDK3_MOUSE	Nucleoside diphosphate kinase 3 (EC 2.7.4.6) (NDK 3) (NDP kinase 3) (Nucleoside diphosphate kinase C ...	0.00	-	vac	0					169
P81766 UniProt NPD GO	NDK3_SPIOL	Nucleoside diphosphate kinase 3 (EC 2.7.4.6) (Nucleoside diphosphate kinase III) (NDK III) (NDP kina ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				153
Q8RXA8 UniProt NPD GO	NDK4_SPIOL	Nucleoside diphosphate kinase 4, chloroplast precursor (EC 2.7.4.6) (Nucleoside diphosphate kinase I ...	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				235
P47919 UniProt NPD GO	NDKA_FLABI	Nucleoside diphosphate kinase A (EC 2.7.4.6) (NDK A) (NDP kinase A)	0.00	-	cyt	0					148
Q05982 UniProt NPD GO	NDKA_RAT	Nucleoside diphosphate kinase A (EC 2.7.4.6) (NDK A) (NDP kinase A) (Tumor metastatic process-associ ...	0.00	-	cyt	0	Cytoplasm. Nucleus	centrosome [IDA]			152
P15532 UniProt NPD GO	NDKA_MOUSE	Nucleoside diphosphate kinase A (EC 2.7.4.6) (NDK A) (NDP kinase A) (Tumor metastatic process-associ ...	0.00	-	cyt	0	Cytoplasm. Nucleus	microsome [IDA] soluble fraction [IDA]			152
P15531 UniProt NPD GO	NDKA_HUMAN	Nucleoside diphosphate kinase A (EC 2.7.4.6) (NDK A) (NDP kinase A) (Tumor metastatic process-associ ...	0.00	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	156490	1UCN	152
Q50KA9 UniProt NPD GO	NDKA_CANFA	Nucleoside diphosphate kinase A (EC 2.7.4.6) (NDK A) (NDP kinase A) (nm23-C1)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				152
P70010 UniProt NPD GO	NDKA1_XENLA	Nucleoside diphosphate kinase A1 (EC 2.7.4.6) (NDK A1) (NDP kinase A1) (NM23/nucleoside diphosphate ...	0.00	-	cyt	0	Cytoplasm (By similarity)				154
P70011 UniProt NPD GO	NDKA2_XENLA	Nucleoside diphosphate kinase A2 (EC 2.7.4.6) (NDK A2) (NDP kinase A2) (NM23/nucleoside diphosphate ...	0.00	-	cyt	0	Cytoplasm (By similarity)				154
P47920 UniProt NPD GO	NDKB_FLABI	Nucleoside diphosphate kinase B (EC 2.7.4.6) (NDK B) (NDP kinase B)	0.00	-	cyt	0					148
P19804 UniProt NPD GO	NDKB_RAT	Nucleoside diphosphate kinase B (EC 2.7.4.6) (NDK B) (NDP kinase B) (P18)	0.00	-	cyt	0	Cytoplasm. Cell membrane	lamellipodium [ISS] ruffle [ISS]			152
P22392 UniProt NPD GO	NDKB_HUMAN	Nucleoside diphosphate kinase B (EC 2.7.4.6) (NDK B) (NDP kinase B) (nm23-H2) (C-myc purine-binding ...	0.00	-	cyt	0	Cytoplasm. Nucleus	lamellipodium [IDA] nucleus [NAS] ruffle [IDA]	156491	1NUE	152
Q01768 UniProt NPD GO	NDKB_MOUSE	Nucleoside diphosphate kinase B (EC 2.7.4.6) (NDK B) (NDP kinase B) (nm23-M2) (P18)	0.00	-	cyt	0	Cytoplasm. Cell membrane	mitochondrion [IDA]			152
P52174 UniProt NPD GO	NDKA_BOVIN	Nucleoside diphosphate kinase NBR-A (EC 2.7.4.6) (NDK NBR-A) (NDP kinase NBR-A)	0.00	-	cyt	0	Cytoplasm. Cell membrane			1BHN	151
P52175 UniProt NPD GO	NDKB_BOVIN	Nucleoside diphosphate kinase NBR-B (EC 2.7.4.6) (NDK NBR-B) (NDP kinase NBR-B)	0.00	-	cyt	0	Cytoplasm. Cell membrane			1BE4	151
P22887 UniProt NPD GO	NDKC_DICDI	Nucleoside diphosphate kinase, cytosolic (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0	Cytoplasm			2BEF	155
P34093 UniProt NPD GO	NDKM_DICDI	Nucleoside diphosphate kinase, mitochondrial precursor (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	mit	0	Mitochondrion; mitochondrial intermembrane space				220
Q6NPD7 UniProt NPD GO	NUD10_ARATH	Nudix hydrolase 10 (EC 3.6.1.-) (AtNUDT10) (ADP-ribose pyrophosphatase) (EC 3.6.1.13) (NADH pyrophos ...	0.00	-	cyt	0					277
Q921I0 UniProt NPD GO	ORML1_MOUSE	ORM1-like protein 1	0.00	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q5R8X5 UniProt NPD GO	ORML1_PONPY	ORM1-like protein 1	0.00	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q5XH57 UniProt NPD GO	ORML1_XENLA	ORM1-like protein 1	0.00	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q9P0S3 UniProt NPD GO	ORML1_HUMAN	ORM1-like protein 1 (Adoplin-1)	0.00	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum	endoplasmic reticulum membrane [IDA]	610073		153
P83951 UniProt NPD GO	OCE1_LEPOE	Ocellatin-1	0.00	-	cyt	0	Secreted protein				25
P83866 UniProt NPD GO	OCE2_LEPOE	Ocellatin-2	0.00	-	cyt	0	Secreted protein				21

You are viewing entries 96051 to 96100 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.