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
P46463 UniProt NPD GO	PEX1_PICPA	Peroxisome biosynthesis protein PAS1 (Peroxin-1)	0.83	-	nuc	0	Cytoplasm (Probable)				1157
P79741 UniProt NPD GO	PESC_BRARE	Pescadillo	0.83	+	mit	0	Nucleus; nucleolus				582
O14356 UniProt NPD GO	TOR1_SCHPO	Phosphatidylinositol 3-kinase tor1 (EC 2.7.1.137) (PtdIns-3-kinase tor1) (PI3-kinase tor1) (PI3K tor ...	0.83	-	end	0					2335
P42951 UniProt NPD GO	LSB6_YEAST	Phosphatidylinositol 4-kinase LSB6 (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase)	0.83	-	nuc	0	Cell membrane; peripheral membrane protein. Vacuole; vacuolar membrane; peripheral membrane protein. ...	cytoplasm [IDA] membrane fraction [IDA] plasma membrane [IDA] vacuolar membrane [IDA]			607
P93025 UniProt NPD GO	PHOT2_ARATH	Phototropin-2 (EC 2.7.11.1) (Defective in chloroplast avoidance protein 1) (Non phototropic hypocoty ...	0.83	-	nuc	0	Cell membrane; peripheral membrane protein				915
Q9I8K3 UniProt NPD GO	PITX3_XENLA	Pituitary homeobox 3 (Homeobox protein PITX3) (xPitx3) (XPitx-3)	0.83	+	nuc	0	Nucleus				292
Q9TTI7 UniProt NPD GO	PIT1_CANFA	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.83	+	nuc	0	Nucleus				291
Q9TST0 UniProt NPD GO	PCGF4_FELCA	Polycomb group RING finger protein 4 (Polycomb complex protein BMI-1)	0.83	-	nuc	0	Nucleus				326
Q8S4P5 UniProt NPD GO	EZ2_MAIZE	Polycomb protein EZ2 (Enhancer of zeste protein 2)	0.83	-	nuc	0	Nucleus (Probable)				894
Q9MZ19 UniProt NPD GO	KCNB1_RABIT	Potassium voltage-gated channel subfamily B member 1 (Voltage-gated potassium channel subunit Kv2.1) ...	0.83	-	nuc	5	Membrane; multi-pass membrane protein				858
Q9BYU1 UniProt NPD GO	PBX4_HUMAN	Pre-B-cell leukemia transcription factor 4 (Homeobox protein PBX4) (Fragment)	0.83	-	nuc	0	Nucleus (Potential)	nucleus [ISS]	608127		330
Q6BLU8 UniProt NPD GO	CWC2_DEBHA	Pre-mRNA-splicing factor CWC2	0.83	+	nuc	0	Nucleus (By similarity)				339
Q6CJQ3 UniProt NPD GO	ISY1_KLULA	Pre-mRNA-splicing factor ISY1	0.83	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				237
Q5AC37 UniProt NPD GO	PRP45_CANAL	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.83	-	exc	0	Nucleus (By similarity)				286
Q7SDY6 UniProt NPD GO	SLU7_NEUCR	Pre-mRNA-splicing factor slu-7	0.83	+	nuc	0	Nucleus (By similarity)				416
Q4WPM6 UniProt NPD GO	SYF2_ASPFU	Pre-mRNA-splicing factor syf2	0.83	-	nuc	0	Nucleus (By similarity)				480
O14511 UniProt NPD GO	NRG2_HUMAN	Pro-neuregulin-2, membrane-bound isoform precursor (Pro-NRG2) [Contains: Neuregulin-2 (NRG-2) (Neura ...	0.83	-	nuc	1	Pro-neuregulin-2, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...		603818		850
Q86TM3 UniProt NPD GO	DDX53_HUMAN	Probable ATP-dependent RNA helicase DDX53 (EC 3.6.1.-) (DEAD box protein 53) (DEAD box protein CAGE) ...	0.83	-	nuc	0	Nucleus				631
O74360 UniProt NPD GO	RGA4_SCHPO	Probable Rho-type GTPase-activating protein 4	0.83	-	nuc	0					933
Q9FG77 UniProt NPD GO	WRKY2_ARATH	Probable WRKY transcription factor 2 (WRKY DNA-binding protein 2)	0.83	-	nuc	0	Nucleus (Probable)				687
O22900 UniProt NPD GO	WRK23_ARATH	Probable WRKY transcription factor 23 (WRKY DNA-binding protein 23)	0.83	-	nuc	0	Nucleus (Probable)				337
Q8VWJ2 UniProt NPD GO	WRK28_ARATH	Probable WRKY transcription factor 28 (WRKY DNA-binding protein 28)	0.83	-	nuc	0	Nucleus (Probable)				318
Q9SR07 UniProt NPD GO	WRK39_ARATH	Probable WRKY transcription factor 39 (WRKY DNA-binding protein 39)	0.83	-	nuc	0	Nucleus (Potential)				330
Q9FL26 UniProt NPD GO	WRKY8_ARATH	Probable WRKY transcription factor 8 (WRKY DNA-binding protein 8)	0.83	+	nuc	0	Nucleus (Probable)				326
Q9SKD7 UniProt NPD GO	CNGC3_ARATH	Probable cyclic nucleotide-gated ion channel 3 (AtCNGC3) (Cyclic nucleotide- and calmodulin-regulate ...	0.83	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				706
Q18007 UniProt NPD GO	ACM1_CAEEL	Probable muscarinic acetylcholine receptor gar-1 (G-protein linked acetylcholine receptor 1)	0.83	-	end	7 *	Membrane; multi-pass membrane protein	postsynaptic membrane [IDA]			713
Q09557 UniProt NPD GO	YQX1_CAEEL	Probable ribosomal protein F34H10.1 in chromosome III	0.83	+	nuc	0					142
Q9USM5 UniProt NPD GO	UBP1_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 1 (EC 3.1.2.15) (Ubiquitin thioesterase 1) (Ubiquitin ...	0.83	+	cyt	0					849
P70398 UniProt NPD GO	USP9X_MOUSE	Probable ubiquitin carboxyl-terminal hydrolase FAF-X (EC 3.1.2.15) (Ubiquitin thioesterase FAF-X) (U ...	0.83	-	end	0		cytoplasm [IDA]			2559
P40985 UniProt NPD GO	HUL4_YEAST	Probable ubiquitin-protein ligase HUL4 (EC 6.3.2.-) (HECT ubiquitin ligase 4)	0.83	-	nuc	0	Nucleus (Probable)				892
P30259 UniProt NPD GO	PRTS4_SCYCA	Protamine S4	0.83	+	nuc	0	Nucleus				32
P02324 UniProt NPD GO	PRTA_ACIST	Protamine-A (Stellin-A) [Contains: Protamine-C (Stellin-C)]	0.83	+	nuc	0	Nucleus				27
P55198 UniProt NPD GO	AF17_HUMAN	Protein AF-17	0.83	+	nuc	0	Nucleus (Potential)		600328		1093
Q6BHS5 UniProt NPD GO	LIC4_DEBHA	Protein ATC1/LIC4	0.83	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				247
Q12365 UniProt NPD GO	BBP1_YEAST	Protein BBP1	0.83	-	nuc	0		spindle pole body [IDA]			385
Q8BGQ1 UniProt NPD GO	CN133_MOUSE	Protein C14orf133 homolog	0.83	-	nuc	0					491
Q5SRN2 UniProt NPD GO	CF010_HUMAN	Protein C6orf10	0.83	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				563
Q8N884 UniProt NPD GO	CF150_HUMAN	Protein C6orf150	0.83	-	nuc	0					522
Q8VDS7 UniProt NPD GO	CF182_MOUSE	Protein C6orf182 homolog	0.83	-	nuc	0					400
Q8K3X0 UniProt NPD GO	CASC3_RAT	Protein CASC3 (Cancer susceptibility candidate gene 3 protein homolog) (Barentsz protein) (Btz)	0.83	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Predominantly. Nucleus (By similarity). Shuttles betw ...				699
Q7T0X5 UniProt NPD GO	CHMP7_XENLA	Protein CHMP7	0.83	+	nuc	0					422
P35659 UniProt NPD GO	DEK_HUMAN	Protein DEK	0.83	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	125264	1Q1V	375
P09534 UniProt NPD GO	DVR1_XENLA	Protein DVR-1 precursor (Vegetal hemisphere VG1 protein) (VG-1)	0.83	+	cyt	0	Secreted protein				360
Q03466 UniProt NPD GO	EBS1_YEAST	Protein EBS1 (EST1-like BCY1 suppressor 1)	0.83	-	nuc	0	Nucleus (Probable)				884
Q922G2 UniProt NPD GO	FA76A_MOUSE	Protein FAM76A	0.83	-	nuc	0					307
P42944 UniProt NPD GO	GZF3_YEAST	Protein GZF3	0.83	-	nuc	0	Nucleus (Potential)	nucleus [IC]			551
Q5ZKD5 UniProt NPD GO	K0690_CHICK	Protein KIAA0690 homolog	0.83	-	end	0	Nucleus; nucleolus (By similarity)				1294
Q5VVJ2 UniProt NPD GO	MYSM1_HUMAN	Protein MYSM1 (Myb-like, SWIRM and MPN domain-containing protein 1)	0.83	-	nuc	0	Nucleus (Probable)			2CU7	828
Q08400 UniProt NPD GO	STE12_KLULA	Protein STE12	0.83	-	nuc	0	Nucleus				666
Q6P1U0 UniProt NPD GO	DONS_XENTR	Protein downstream neighbor of son homolog	0.83	-	nuc	0	Nucleus (By similarity)				577

You are viewing entries 7501 to 7550 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.