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
Q5HZG4 UniProt NPD GO	TAF3_MOUSE	Transcription initiation factor TFIID subunit 3 (TBP-associated factor 3) (Transcription initiation ...	0.95	+	nuc	0	Nucleus (By similarity)				932
Q99PP7 UniProt NPD GO	TIF1G_MOUSE	Transcription intermediary factor 1-gamma (TIF1-gamma) (Tripartite motif-containing protein 33)	0.95	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			1142
Q9BYV9 UniProt NPD GO	BACH2_HUMAN	Transcription regulator protein BACH2 (BTB and CNC homolog 2)	0.95	+	nuc	0	Nucleus (By similarity)		605394		841
P14064 UniProt NPD GO	HAP4_YEAST	Transcriptional activator HAP4	0.95	-	nuc	0	Nucleus	CCAAT-binding factor complex [TAS]			554
Q04779 UniProt NPD GO	RCO1_YEAST	Transcriptional regulatory protein RCO1	0.95	+	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			684
P39001 UniProt NPD GO	UME6_YEAST	Transcriptional regulatory protein UME6 (Unscheduled meiotic gene expression protein 6) (Negative tr ...	0.95	+	nuc	0	Nucleus	nucleus [IPI]			836
O95359 UniProt NPD GO	TACC2_HUMAN	Transforming acidic coiled-coil-containing protein 2 (Anti Zuai-1) (AZU-1)	0.95	-	nuc	0	Nucleus. Centrosome. Concentrated at centrosomes		605302		1026
Q8CIR4 UniProt NPD GO	TRPM6_MOUSE	Transient receptor potential cation channel subfamily M member 6 (EC 2.7.11.1) (Channel kinase 2) (M ...	0.95	-	end	6	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] brush border membrane [IDA]			2028
P37709 UniProt NPD GO	TRHY_RABIT	Trichohyalin	0.95	+	nuc	0					1407
P50586 UniProt NPD GO	TUB_MOUSE	Tubby protein	0.95	+	nuc	0		cytosol [IMP]		1C8Z	505
O88808 UniProt NPD GO	TUB_RAT	Tubby protein homolog	0.95	+	nuc	0					505
P25446 UniProt NPD GO	TNR6_MOUSE	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.95	+	exc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			327
P35991 UniProt NPD GO	BTK_MOUSE	Tyrosine-protein kinase BTK (EC 2.7.10.2) (Bruton tyrosine kinase) (Agammaglobulinaemia tyrosine kin ...	0.95	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasmic vesicle [IDA]			658
P09406 UniProt NPD GO	RU17_XENLA	U1 small nuclear ribonucleoprotein 70 kDa (U1 snRNP 70 kDa) (snRNP70) (U1-70K)	0.95	+	nuc	0					471
Q5TAP6 UniProt NPD GO	UT14C_HUMAN	U3 small nucleolar RNA-associated protein 14 homolog C	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)		608969		766
P40079 UniProt NPD GO	LCP5_YEAST	U3 small nucleolar ribonucleoprotein protein LCP5	0.95	-	nuc	0	Nucleus; nucleolus	small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [TAS]			357
Q03338 UniProt NPD GO	PRP3_YEAST	U4/U6 small nuclear ribonucleoprotein PRP3 (Pre-mRNA-splicing factor 3)	0.95	+	nuc	0	Nucleus	U4/U6 x U5 tri-snRNP complex [IDA]			469
Q9Z315 UniProt NPD GO	SNUT1_MOUSE	U4/U6.U5 tri-snRNP-associated protein 1 (Squamous cell carcinoma antigen recognized by T-cells 1) (S ...	0.95	+	nuc	0	Nucleus (By similarity)				806
O43290 UniProt NPD GO	SNUT1_HUMAN	U4/U6.U5 tri-snRNP-associated protein 1 (U4/U6.U5 tri-snRNP-associated 110 kDa protein) (Squamous ce ...	0.95	+	nuc	0	Nucleus. Found in the nucleus of mitogen-activated peripheral blood mononuclear cells (PBMCs), tumor ...	cytoplasm [TAS] cytosol [TAS]	605941		800
P53914 UniProt NPD GO	YNN2_YEAST	UPF0202 protein YNL132W	0.95	-	nuc	0	Nucleus (By similarity)	nucleolus [IDA]			1056
Q5I043 UniProt NPD GO	UBP28_MOUSE	Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.1.2.15) (Ubiquitin thioesterase 28) (Ubiquitin-specif ...	0.95	+	nuc	0					1051
Q70CQ1 UniProt NPD GO	UBP49_HUMAN	Ubiquitin carboxyl-terminal hydrolase 49 (EC 3.1.2.15) (Ubiquitin thioesterase 49) (Ubiquitin-specif ...	0.95	+	nuc	0					688
Q7TPV2 UniProt NPD GO	DZIP3_MOUSE	Ubiquitin ligase protein DZIP3 (EC 6.3.2.-) (DAZ-interacting protein 3 homolog)	0.95	-	nuc	0	Cytoplasm (By similarity)				1204
Q86Y13 UniProt NPD GO	DZIP3_HUMAN	Ubiquitin ligase protein DZIP3 (EC 6.3.2.-) (DAZ-interacting protein 3) (RNA-binding ubiquitin ligas ...	0.95	-	nuc	0	Cytoplasm	cytoplasm [IDA]	608672		1208
Q8VC56 UniProt NPD GO	RNF8_MOUSE	Ubiquitin ligase protein RNF8 (EC 6.3.2.-) (RING finger protein 8) (AIP37) (ActA-interacting protein ...	0.95	-	nuc	0	Nucleus (By similarity)				488
P43254 UniProt NPD GO	COP1_ARATH	Ubiquitin-protein ligase COP1 (EC 6.3.2.-) (Constitutive photomorphogenesis protein 1)	0.95	+	nuc	0	Nucleus. Cytoplasm. Localizes to the nucleus in darkness but is gradually relocated to the cytoplasm ...				675
O42354 UniProt NPD GO	MDM2_BRARE	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Double minute 2 protein)	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				445
P56950 UniProt NPD GO	MDM2_CANFA	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Double minute 2 protein) ( ...	0.95	-	nuc	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Expressed predominantly in the nucl ...				487
O95071 UniProt NPD GO	EDD1_HUMAN	Ubiquitin-protein ligase EDD1 (EC 6.3.2.-) (Hyperplastic discs protein homolog) (hHYD) (Progestin-in ...	0.95	-	nuc	0	Nucleus	nucleus [IDA] soluble fraction [TAS]	608413	1I2T	2799
P28003 UniProt NPD GO	YAD4_YEAST	Uncharacterized protein FUN19	0.95	-	nuc	0					413
P38277 UniProt NPD GO	YBY8_YEAST	Uncharacterized protein YBR138C	0.95	-	nuc	0		cytoplasm [IDA]			524
P40061 UniProt NPD GO	YES3_YEAST	Uncharacterized protein YER093C	0.95	-	mit	0	Membrane; multi-pass membrane protein (Potential)	TORC 2 complex [IPI]			1430
P53127 UniProt NPD GO	YGN1_YEAST	Uncharacterized protein YGL131C	0.95	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			1403
P53278 UniProt NPD GO	YG3A_YEAST	Uncharacterized protein YGR130C	0.95	-	nuc	0		cytoplasm [IDA]			816
P40563 UniProt NPD GO	YIS3_YEAST	Uncharacterized protein YIR003W	0.95	-	nuc	0	Actin patch. Cortical actin patches	actin cytoskeleton [IDA]			679
P47030 UniProt NPD GO	YJI3_YEAST	Uncharacterized protein YJL083W	0.95	+	nuc	0					604
P42846 UniProt NPD GO	YN48_YEAST	Uncharacterized protein YNL308C	0.95	+	nuc	0		nucleolus [IDA]			591
Q9VKM6 UniProt NPD GO	VPS72_DROME	Vacuolar protein sorting protein 72 homolog (Protein YL-1)	0.95	+	nuc	0	Nucleus (By similarity)	TIP60 histone acetyltransferase complex [IPI]			351
P47810 UniProt NPD GO	WEE1_MOUSE	Wee1-like protein kinase (EC 2.7.10.2)	0.95	-	nuc	0	Nucleus (By similarity)				646
Q9GLM3 UniProt NPD GO	RPGR1_BOVIN	X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGR-interacting protein 1)	0.95	-	nuc	0	Situated between the axonemal microtubules and the plasma membrane (By similarity)				1221
Q9QY02 UniProt NPD GO	YTDC1_RAT	YTH domain-containing protein 1 (Putative splicing factor YT521) (RA301-binding protein)	0.95	+	nuc	0	Nucleus. Localizes to a novel subnuclear structure, the YT bodies	nuclear body [IDA] nucleoplasm [IDA]			738
Q6DCD7 UniProt NPD GO	ZCHC4_XENLA	Zinc finger CCHC domain-containing protein 4	0.95	+	nuc	0					489
Q52KB5 UniProt NPD GO	ZBT24_BRARE	Zinc finger and BTB domain-containing protein 24	0.95	+	nuc	0	Nucleus (Potential)	nucleus [IC]			672
P52746 UniProt NPD GO	ZN142_HUMAN	Zinc finger protein 142 (HA4654)	0.95	+	nuc	0	Nucleus (Potential)		604083		1687
P28167 UniProt NPD GO	ZFH2_DROME	Zinc finger protein 2 (Zinc finger homeodomain protein 2)	0.95	-	nuc	0	Nucleus (Probable)				3005
Q9Y2X9 UniProt NPD GO	ZN281_HUMAN	Zinc finger protein 281 (Zinc finger DNA-binding protein 99) (Transcription factor ZBP-99) (GC-box-b ...	0.95	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]			895
Q9N003 UniProt NPD GO	ZN425_MACFA	Zinc finger protein 425 (Fragment)	0.95	-	nuc	0	Nucleus (Probable)				741
P59923 UniProt NPD GO	ZN445_HUMAN	Zinc finger protein 445	0.95	-	nuc	0	Nucleus (Potential)				1031
Q96IT1 UniProt NPD GO	ZN496_HUMAN	Zinc finger protein 496	0.95	-	nuc	0	Nucleus (Probable)				587
Q96ME7 UniProt NPD GO	ZN512_HUMAN	Zinc finger protein 512	0.95	+	nuc	0	Nucleus (Potential)			2CTD	567

You are viewing entries 2151 to 2200 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.