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
Q9EP82 UniProt NPD GO	WDR4_MOUSE	WD repeat protein 4	0.61	+	nuc	0					413
Q15061 UniProt NPD GO	WDR43_HUMAN	WD repeat protein 43	0.61	-	nuc	0	Nucleus; nucleolus				720
Q96MR6 UniProt NPD GO	WDR65_HUMAN	WD repeat protein 65	0.61	-	cyt	0	Membrane; single-pass type IV membrane protein (Potential)				698
Q9SU78 UniProt NPD GO	MSI5_ARATH	WD-40 repeat protein MSI5	0.61	-	nuc	0	Nucleus (By similarity)				487
Q9FKP8 UniProt NPD GO	Y5541_ARATH	ZF-HD homeobox protein At5g65410	0.61	-	nuc	0	Nucleus (Probable)			1WH5	279
Q5RJC5 UniProt NPD GO	ZFNL5_ARATH	Zinc finger CCCH domain-containing protein ZFN-like 5	0.61	-	nuc	0	Nucleus (By similarity)				435
Q9HCC9 UniProt NPD GO	ZFY28_HUMAN	Zinc finger FYVE domain-containing protein 28	0.61	-	nuc	0					887
Q8K088 UniProt NPD GO	ZN482_MOUSE	Zinc finger and BTB domain-containing protein 6 (Zinc finger protein 482)	0.61	-	nuc	0	Nucleus (By similarity)				423
Q8IYN0 UniProt NPD GO	ZN100_HUMAN	Zinc finger protein 100	0.61	-	nuc	0	Nucleus (Probable)		603982		542
O15535 UniProt NPD GO	ZN193_HUMAN	Zinc finger protein 193 (PRD51) (Zinc finger and SCAN domain-containing protein 9)	0.61	-	nuc	0	Nucleus (Potential)		602246		394
O95125 UniProt NPD GO	ZN202_HUMAN	Zinc finger protein 202	0.61	+	nuc	0	Nucleus		603430		648
Q14593 UniProt NPD GO	ZN273_HUMAN	Zinc finger protein 273 (Zinc finger protein HZF9)	0.61	-	nuc	0	Nucleus (Probable)		604756		504
Q969J2 UniProt NPD GO	ZN307_HUMAN	Zinc finger protein 307 (P373c6.1)	0.61	-	nuc	0	Nucleus (Probable)				545
Q9BYN7 UniProt NPD GO	ZN341_HUMAN	Zinc finger protein 341	0.61	+	nuc	0	Nucleus (Probable)				854
Q96NI8 UniProt NPD GO	ZN570_HUMAN	Zinc finger protein 570	0.61	-	nuc	0	Nucleus (Potential)				536
Q8N2I2 UniProt NPD GO	ZN619_HUMAN	Zinc finger protein 619	0.61	-	nuc	0	Nucleus (Probable)				560
Q3TDE8 UniProt NPD GO	ZN691_MOUSE	Zinc finger protein 691	0.61	-	nuc	0	Nucleus (Probable)				283
Q39266 UniProt NPD GO	ZFP7_ARATH	Zinc finger protein 7	0.61	-	nuc	0					209
Q8BGS3 UniProt NPD GO	ZKSC1_MOUSE	Zinc finger with KRAB and SCAN domain-containing protein 1	0.61	-	nuc	0	Nucleus (Potential)				561
Q755D0 UniProt NPD GO	MCE1_ASHGO	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.61	+	nuc	0	Nucleus (By similarity)				463
Q9UVF5 UniProt NPD GO	PALF_YARLI	pH-response regulator protein palF/RIM8	0.61	-	nuc	0					881
P53072 UniProt NPD GO	TAN1_YEAST	tRNA acetyltransferase TAN1 (EC 2.3.-.-)	0.61	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			289
O81191 UniProt NPD GO	SCS_SALOF	1,8-cineole synthase, chloroplast precursor (EC 4.2.3.-) (SCS)	0.60	-	mit	0	Plastid; chloroplast				591
Q42881 UniProt NPD GO	1A13_LYCES	1-aminocyclopropane-1-carboxylate synthase 3 (EC 4.4.1.14) (ACC synthase 3) (S-adenosyl-L-methionine ...	0.60	-	nuc	0					469
P51178 UniProt NPD GO	PLCD1_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.60	-	nuc	0			602142		756
Q9Y4L1 UniProt NPD GO	OXRP_HUMAN	150 kDa oxygen-regulated protein precursor (Orp150) (Hypoxia up-regulated 1)	0.60	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]	601746		999
Q9D338 UniProt NPD GO	RM19_MOUSE	39S ribosomal protein L19, mitochondrial precursor (L19mt) (MRP-L19)	0.60	-	mit	0	Mitochondrion				292
Q9V9Z1 UniProt NPD GO	RM32_DROME	39S ribosomal protein L32, mitochondrial precursor	0.60	-	nuc	0	Mitochondrion				195
Q26486 UniProt NPD GO	FKBP4_SPOFR	46 kDa FK506-binding nuclear protein (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Ro ...	0.60	-	nuc	0	Nucleus				412
Q962U1 UniProt NPD GO	RL13_SPOFR	60S ribosomal protein L13	0.60	-	nuc	0					219
O48513 UniProt NPD GO	RL13_CHLSW	60S ribosomal protein L13 (BBC1 protein homolog)	0.60	-	nuc	0					208
Q95043 UniProt NPD GO	RL13_SCHMA	60S ribosomal protein L13 (BBC1 protein homolog)	0.60	-	nuc	0					184
Q7T3P0 UniProt NPD GO	RL15_HYPNO	60S ribosomal protein L15	0.60	-	mit	0					203
Q7T3N4 UniProt NPD GO	RL15_MEGAM	60S ribosomal protein L15	0.60	-	mit	0					203
P09897 UniProt NPD GO	RL18A_XENLA	60S ribosomal protein L18-A (L14A)	0.60	-	nuc	0	Cytoplasm				187
P02412 UniProt NPD GO	RL18B_XENLA	60S ribosomal protein L18-B (L14B)	0.60	-	nuc	0	Cytoplasm				187
Q7Z0T8 UniProt NPD GO	RL24_SCHJA	60S ribosomal protein L24	0.60	-	nuc	0					156
P50880 UniProt NPD GO	RL3_CAEEL	60S ribosomal protein L3	0.60	-	mit	0	Cytoplasm				401
Q3MHM7 UniProt NPD GO	RL35_BOVIN	60S ribosomal protein L35	0.60	-	nuc	0					122
Q6UZF7 UniProt NPD GO	RL35_HIPCM	60S ribosomal protein L35	0.60	-	nuc	0					122
P50878 UniProt NPD GO	RL4_RAT	60S ribosomal protein L4 (L1)	0.60	+	nuc	0					420
P17843 UniProt NPD GO	RL44_TRYBB	60S ribosomal protein L44	0.60	-	nuc	0	Cytoplasm				105
Q02878 UniProt NPD GO	RL6_HUMAN	60S ribosomal protein L6 (TAX-responsive enhancer element-binding protein 107) (TAXREB107) (Neoplasm ...	0.60	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	603703		287
Q61824 UniProt NPD GO	ADA12_MOUSE	ADAM 12 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 12) (Meltrin alpha)	0.60	-	nuc	1	Membrane; single-pass type I membrane protein				903
Q9XSL6 UniProt NPD GO	ADA28_MACFA	ADAM 28 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 28) (eMDC II)	0.60	-	end	1	Membrane; single-pass type I membrane protein				776
O75173 UniProt NPD GO	ATS4_HUMAN	ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metalloproteinase with thrombospondin motifs 4) ...	0.60	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)		603876		837
Q9NZ52 UniProt NPD GO	GGA3_HUMAN	ADP-ribosylation factor-binding protein GGA3 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.60	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	Golgi trans face [IDA]	606006	1YD8	723
P22892 UniProt NPD GO	AP1G1_MOUSE	AP-1 complex subunit gamma-1 (Adapter-related protein complex 1 gamma-1 subunit) (Gamma-adaptin) (Ad ...	0.60	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [IDA] perinuclear region [IDA]		2A7B	821
Q9UPM8 UniProt NPD GO	AP4E1_HUMAN	AP-4 complex subunit epsilon-1 (Adapter-related protein complex 4 epsilon-1 subunit) (Epsilon subuni ...	0.60	-	cyt	0	Golgi apparatus; trans-Golgi network. Associated with the trans-Golgi network. Found in soma and den ...		607244		1137
Q74ZC1 UniProt NPD GO	DBP9_ASHGO	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.60	-	nuc	0	Nucleus; nucleolus (By similarity)				595

You are viewing entries 18851 to 18900 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.