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
P63276 UniProt NPD GO	RS17_MOUSE	40S ribosomal protein S17	0.16	-	nuc	0					134
Q6QAP7 UniProt NPD GO	RS17_PIG	40S ribosomal protein S17	0.16	-	nuc	0					134
P04644 UniProt NPD GO	RS17_RAT	40S ribosomal protein S17	0.16	-	mit	0					134
P25443 UniProt NPD GO	RS2_YEAST	40S ribosomal protein S2 (S4) (YS5) (RP12) (Omnipotent suppressor protein SUP44)	0.16	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]		1K5X	253
Q6RF66 UniProt NPD GO	RS21_PECGU	40S ribosomal protein S21	0.16	-	nuc	0					85
Q7SC06 UniProt NPD GO	RS25_NEUCR	40S ribosomal protein S25	0.16	-	nuc	0					97
P41057 UniProt NPD GO	RS29A_YEAST	40S ribosomal protein S29-A (S36) (YS29)	0.16	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			55
O22424 UniProt NPD GO	RS4_MAIZE	40S ribosomal protein S4	0.16	-	mit	0	Cytoplasm				265
Q9P3T6 UniProt NPD GO	RS5B_SCHPO	40S ribosomal protein S5-B	0.16	-	cyt	0					203
Q24186 UniProt NPD GO	RS5A_DROME	40S ribosomal protein S5a	0.16	-	cyt	0					228
Q23312 UniProt NPD GO	RS7_CAEEL	40S ribosomal protein S7	0.16	-	nuc	0					194
P13731 UniProt NPD GO	HSP47_CHICK	47 kDa heat shock protein precursor (Collagen-binding protein 1)	0.16	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				405
Q9XT75 UniProt NPD GO	HEM0_DELLE	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				582
O94069 UniProt NPD GO	HEM1_CANAL	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				564
P09950 UniProt NPD GO	HEM1_YEAST	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.16	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			548
P28334 UniProt NPD GO	5HT1B_MOUSE	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				386
P50129 UniProt NPD GO	5HT2A_PIG	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2) (5-HT2A)	0.16	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				470
P30994 UniProt NPD GO	5HT2B_RAT	5-hydroxytryptamine 2B receptor (5-HT-2B) (Serotonin receptor 2B) (5-HT-2F) (Stomach fundus serotoni ...	0.16	-	vac	7	Membrane; multi-pass membrane protein				479
O70528 UniProt NPD GO	5HT4R_CAVPO	5-hydroxytryptamine 4 receptor (5-HT-4) (Serotonin receptor 4) (5-HT4)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				388
O04603 UniProt NPD GO	RK5_ARATH	50S ribosomal protein L5, chloroplast precursor	0.16	-	mit	0	Plastid; chloroplast	cytosolic ribosome (sensu Eukaryota) [IDA]			262
P80783 UniProt NPD GO	CWP06_TOBAC	56 kDa cell wall protein (Fragment)	0.16	-		0	Cell wall				18
Q85G22 UniProt NPD GO	CH60_CYAME	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.16	-	mit	0	Plastid; chloroplast				526
P53030 UniProt NPD GO	RL1_YEAST	60S ribosomal protein L1 (L10a)	0.16	+	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	217
P45636 UniProt NPD GO	RL102_ORYSA	60S ribosomal protein L10-2 (Putative tumor suppressor SG12) (Protein QM1)	0.16	-	mit	0					219
Q9NBJ7 UniProt NPD GO	RL10A_CAERE	60S ribosomal protein L10a (Fragment)	0.16	+	nuc	0					112
Q962U2 UniProt NPD GO	RL11_SPOFR	60S ribosomal protein L11	0.16	-	nuc	0					195
P61284 UniProt NPD GO	RL12_BOVIN	60S ribosomal protein L12	0.16	-	nuc	0					165
Q6QMZ7 UniProt NPD GO	RL12_CHILA	60S ribosomal protein L12	0.16	-	nuc	0					165
P30050 UniProt NPD GO	RL12_HUMAN	60S ribosomal protein L12	0.16	-	nuc	0			180475		165
Q9CR57 UniProt NPD GO	RL14_MOUSE	60S ribosomal protein L14	0.16	-	nuc	0					216
P50914 UniProt NPD GO	RL14_HUMAN	60S ribosomal protein L14 (CAG-ISL 7)	0.16	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			212
O42991 UniProt NPD GO	RL16B_SCHPO	60S ribosomal protein L16-B	0.16	-	cyt	0					197
Q6C9C4 UniProt NPD GO	RM02_YARLI	60S ribosomal protein L2, mitochondrial precursor	0.16	-	mit	0	Mitochondrion (By similarity)				374
Q94776 UniProt NPD GO	RL23_TRYCR	60S ribosomal protein L23 (L17) (TCEST082)	0.16	-	mit	0					141
Q7ZV82 UniProt NPD GO	RL27_BRARE	60S ribosomal protein L27	0.16	-	cyt	0					135
O82204 UniProt NPD GO	RL281_ARATH	60S ribosomal protein L28-1	0.16	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			143
Q9U2A8 UniProt NPD GO	RL37A_CAEEL	60S ribosomal protein L37a	0.16	-	cyt	0					90
Q29375 UniProt NPD GO	RL7A_PIG	60S ribosomal protein L7a (Fragment)	0.16	-	nuc	0					132
Q38931 UniProt NPD GO	FKB70_ARATH	70 kDa peptidyl-prolyl isomerase (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotama ...	0.16	-	cyt	0					551
Q6BZH1 UniProt NPD GO	GRP78_DEBHA	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.16	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				683
Q9FLT4 UniProt NPD GO	ATH14_ARATH	ABC2 homolog 14	0.16	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				907
Q8R534 UniProt NPD GO	ADM1B_MOUSE	ADAM 1b precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 1b) (Fertilin alpha 1b s ...	0.16	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			806
Q9R159 UniProt NPD GO	ADA25_MOUSE	ADAM 25 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 25) (Testase 2)	0.16	-	nuc	1	Membrane; single-pass type I membrane protein				760
P51644 UniProt NPD GO	ARF4_XENLA	ADP-ribosylation factor 4	0.16	-	mit	0					179
O97628 UniProt NPD GO	AIP_CERAE	AH receptor-interacting protein (AIP) (Aryl-hydrocarbon receptor-interacting protein) (HBV-X-associa ...	0.16	-	cyt	0	Cytoplasm				330
P00978 UniProt NPD GO	AMBP_BOVIN	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.16	-	exc	0	Secreted protein	extracellular region [ISS] plasma membrane [ISS]			352
Q75F71 UniProt NPD GO	AP3S_ASHGO	AP-3 complex subunit sigma (Adapter-related protein complex 3 sigma subunit) (Sigma-adaptin 3A) (AP- ...	0.16	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				185
Q9XZ63 UniProt NPD GO	ARMET_DROME	ARMET-like protein precursor	0.16	-	exc	0	Secreted protein (Potential)				173
Q6EUN0 UniProt NPD GO	ASCL1_ORYSA	ASC1-like protein 1 (Alternaria stem canker resistance-like protein 1)	0.16	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				309
P13621 UniProt NPD GO	ATPO_BOVIN	ATP synthase O subunit, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.16	-	mit	0	Mitochondrion			2BO5	213

You are viewing entries 55201 to 55250 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.