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
Q2U9B0 UniProt NPD GO	BRE1_ASPOR	Ubiquitin-protein ligase bre1 (EC 6.3.2.-)	0.80	-	nuc	0	Nucleus (By similarity)				760
P53940 UniProt NPD GO	YNH7_YEAST	Uncharacterized J domain-containing protein YNL077W	0.80	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			528
P40361 UniProt NPD GO	YJH0_YEAST	Uncharacterized deaminase YJL070C (EC 3.5.4.-)	0.80	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			888
Q05863 UniProt NPD GO	YL281_YEAST	Uncharacterized peptide chain release factor-like protein YLR281C, mitochondrial precursor	0.80	-	nuc	0	Mitochondrion	mitochondrion [IDA]			155
Q96LQ0 UniProt NPD GO	CN050_HUMAN	Uncharacterized protein C14orf50	0.80	-	cyt	0					422
Q8NDZ0 UniProt NPD GO	CX020_HUMAN	Uncharacterized protein CXorf20	0.80	-	nuc	0					799
P40007 UniProt NPD GO	YEJ2_YEAST	Uncharacterized protein YER002W	0.80	-	nuc	0		nucleolus [IDA] nucleus [IDA]			231
P53207 UniProt NPD GO	YG18_YEAST	Uncharacterized protein YGR013W	0.80	-	nuc	0		snRNP U1 [IDA]			620
P53244 UniProt NPD GO	YG2B_YEAST	Uncharacterized protein YGR068C	0.80	-	nuc	0					586
P38814 UniProt NPD GO	YHQ3_YEAST	Uncharacterized protein YHR103W	0.80	-	nuc	0		cytoplasm [IDA]			852
Q9NZI7 UniProt NPD GO	UBIP1_HUMAN	Upstream-binding protein 1 (LBP-1)	0.80	-	nuc	0	Nucleus		609784		540
Q811S7 UniProt NPD GO	UBIP1_MOUSE	Upstream-binding protein 1 (Nuclear factor 2d9) (NF2d9)	0.80	-	nuc	0	Nucleus (By similarity)				540
P34110 UniProt NPD GO	VPS35_YEAST	Vacuolar protein sorting-associated protein VPS35	0.80	-	nuc	0	Membrane; peripheral membrane protein	endosome [IPI] retromer complex [TAS]			944
Q9JLZ9 UniProt NPD GO	VAX2_RAT	Ventral anterior homeobox 2	0.80	+	nuc	0	Nucleus (Probable)				292
Q8WQ85 UniProt NPD GO	VILD_DICDI	Villidin	0.80	-	nuc	0	Membrane; peripheral membrane protein. Associated with membranes and the cytoskeleton				1704
Q94637 UniProt NPD GO	VIT6_OSCBR	Vitellogenin-6 precursor	0.80	-	exc	0	Secreted protein				1660
O73700 UniProt NPD GO	CAC1D_CHICK	Voltage-dependent L-type calcium channel subunit alpha-1D (Voltage-gated calcium channel subunit alp ...	0.80	+	end	21	Membrane; multi-pass membrane protein				2190
Q9Y6W5 UniProt NPD GO	WASF2_HUMAN	Wiskott-Aldrich syndrome protein family member 2 (WASP-family protein member 2) (Protein WAVE-2) (Ve ...	0.80	+	nuc	0	Cytoplasm (By similarity). At the interface between the lamellipodial actin meshwork and the membran ...	actin cytoskeleton [TAS]	605875	2A40	498
P40105 UniProt NPD GO	YRF12_YEAST	Y'helicase protein 1 copy 2 (EC 3.6.1.-)	0.80	+	nuc	0					1681
O13559 UniProt NPD GO	YRF14_YEAST	Y'helicase protein 1 copy 4 (EC 3.6.1.-)	0.80	+	nuc	0					1382
Q8K3Y6 UniProt NPD GO	ZCC2_RAT	Zinc finger CCCH type antiviral protein 1 (rZAP)	0.80	-	nuc	0	Nucleus (Potential)				776
Q8R1J3 UniProt NPD GO	ZCHC9_MOUSE	Zinc finger CCHC domain-containing protein 9	0.80	+	nuc	0					273
Q91VL9 UniProt NPD GO	ZBTB1_MOUSE	Zinc finger and BTB domain-containing protein 1	0.80	-	nuc	0	Nucleus (Potential)				713
Q8N680 UniProt NPD GO	ZBTB2_HUMAN	Zinc finger and BTB domain-containing protein 2	0.80	-	nuc	0	Nucleus (Potential)				514
Q9BUG6 UniProt NPD GO	ZSCA5_HUMAN	Zinc finger and SCAN domain-containing protein 5 (Zinc finger protein 495)	0.80	-	nuc	0	Nucleus (Potential)				496
P28166 UniProt NPD GO	ZFH1_DROME	Zinc finger protein 1 (Zinc finger homeodomain protein 1)	0.80	-	nuc	0	Nucleus (Probable)				1054
Q4R4C7 UniProt NPD GO	ZNF14_MACFA	Zinc finger protein 14	0.80	-	nuc	0	Nucleus (Probable)				642
O88291 UniProt NPD GO	ZN326_MOUSE	Zinc finger protein 326 (Zinc finger protein-associated with nuclear matrix of 75 kDa)	0.80	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix	insoluble fraction [IDA] nuclear matrix [IDA] nucleus [IDA]			580
Q8N823 UniProt NPD GO	ZN611_HUMAN	Zinc finger protein 611	0.80	-	nuc	0	Nucleus (Probable)				705
Q91690 UniProt NPD GO	GLI1_XENLA	Zinc finger protein GLI1 (GLI-1) (Fragment)	0.80	-	nuc	0	Nucleus				1360
P39959 UniProt NPD GO	YEW0_YEAST	Zinc finger protein YER130C	0.80	-	nuc	0	Nucleus (Potential)				443
O16977 UniProt NPD GO	NAS32_CAEEL	Zinc metalloproteinase nas-32 precursor (EC 3.4.24.21) (Nematode astacin 32)	0.80	+	exc	0	Secreted protein (Potential)				651
Q02084 UniProt NPD GO	A33_PLEWA	Zinc-binding protein A33	0.80	+	nuc	0	Nucleus				624
P27925 UniProt NPD GO	CREB1_BOVIN	cAMP response element-binding protein (CREB) (Cyclic AMP-responsive DNA-binding protein)	0.80	+	nuc	0	Nucleus				325
Q63085 UniProt NPD GO	PDE3B_RAT	cGMP-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) (Cyclic GMP-inhibited phosphodiesteras ...	0.80	+	end	5	Membrane; peripheral membrane protein (Potential)				1108
Q6BT58 UniProt NPD GO	MCE1_DEBHA	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.80	-	nuc	0	Nucleus (By similarity)				458
Q6CWQ8 UniProt NPD GO	PUS1_KLULA	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.80	-	nuc	0	Nucleus (By similarity)				553
P24135 UniProt NPD GO	PLCG2_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 2 (EC 3.1.4.11) (Phosphoinositide ph ...	0.79	-	cyt	0					1265
P16320 UniProt NPD GO	NOF_DROME	120.7 kDa protein in NOF-FB transposable element	0.79	-	nuc	0	Nucleus (Probable)				1056
Q6CM04 UniProt NPD GO	RS6_KLULA	40S ribosomal protein S6	0.79	-	nuc	0					236
Q7SYU0 UniProt NPD GO	RS8_XENLA	40S ribosomal protein S8	0.79	+	nuc	0					207
O43422 UniProt NPD GO	P52K_HUMAN	52 kDa repressor of the inhibitor of the protein kinase (p58IPK-interacting protein) (58 kDa interfe ...	0.79	+	mit	0			607374		761
P36241 UniProt NPD GO	RL19_DROME	60S ribosomal protein L19	0.79	-	nuc	0					203
P46779 UniProt NPD GO	RL28_HUMAN	60S ribosomal protein L28	0.79	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	603638		136
P34040 UniProt NPD GO	RL32_TRIHA	60S ribosomal protein L32	0.79	-	nuc	0					137
P84312 UniProt NPD GO	RL32_DROBF	60S ribosomal protein L32 (Ribosomal protein 49)	0.79	-	nuc	0					134
P84314 UniProt NPD GO	RL32_DROGU	60S ribosomal protein L32 (Ribosomal protein 49)	0.79	-	nuc	0					134
P84313 UniProt NPD GO	RL32_DROMD	60S ribosomal protein L32 (Ribosomal protein 49)	0.79	-	nuc	0					134
P84311 UniProt NPD GO	RL32_DROSU	60S ribosomal protein L32 (Ribosomal protein 49)	0.79	-	nuc	0					134
Q90YT1 UniProt NPD GO	RL37_ICTPU	60S ribosomal protein L37	0.79	-	mit	0					96

You are viewing entries 9201 to 9250 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.