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
Q7M3Y3 UniProt NPD GO	TNNI_CHLNI	Troponin I (TnI)	0.92	+	nuc	0					292
P19351 UniProt NPD GO	TNNT_DROME	Troponin T, skeletal muscle (Protein upheld) (Protein intended thorax)	0.92	-	nuc	0					397
O00295 UniProt NPD GO	TULP2_HUMAN	Tubby-related protein 2 (Tubby-like protein 2)	0.92	+	nuc	0			602309		520
P13903 UniProt NPD GO	TWIST_XENLA	Twist-related protein (T18) (X-twist)	0.92	-	nuc	0	Nucleus				166
P54637 UniProt NPD GO	PTP3_DICDI	Tyrosine-protein phosphatase 3 (EC 3.1.3.48) (Protein-tyrosine-phosphate phosphohydrolase 3)	0.92	-	nuc	0	Cytoplasm				989
Q64512 UniProt NPD GO	PTN13_MOUSE	Tyrosine-protein phosphatase non-receptor type 13 (EC 3.1.3.48) (Protein tyrosine phosphatase PTP-BL ...	0.92	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]		1VJ6	2453
P38319 UniProt NPD GO	TYDP1_YEAST	Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) (Tyr-DNA phosphodiesterase 1)	0.92	+	nuc	0	Nucleus	nucleus [IDA]		1Q32	544
Q66II8 UniProt NPD GO	RU17_XENTR	U1 small nuclear ribonucleoprotein 70 kDa (U1 snRNP 70 kDa) (snRNP70) (U1-70K)	0.92	+	nuc	0					471
Q8VCH8 UniProt NPD GO	UBXD2_MOUSE	UBX domain-containing protein 2	0.92	+	nuc	0					506
Q96CS3 UniProt NPD GO	UBXD8_HUMAN	UBX domain-containing protein 8 (Protein ETEA)	0.92	+	nuc	0	Cytoplasm				445
Q99MX1 UniProt NPD GO	UBP26_MOUSE	Ubiquitin carboxyl-terminal hydrolase 26 (EC 3.1.2.15) (Ubiquitin thioesterase 26) (Ubiquitin-specif ...	0.92	-	nuc	0					835
Q8TEY7 UniProt NPD GO	UBP33_HUMAN	Ubiquitin carboxyl-terminal hydrolase 33 (EC 3.1.2.15) (Ubiquitin thioesterase 33) (Ubiquitin-specif ...	0.92	-	nuc	0		cytoplasm [TAS] VCB complex [TAS]			942
O13769 UniProt NPD GO	ULP2_SCHPO	Ubiquitin-like-specific protease 2 (EC 3.4.22.-)	0.92	-	nuc	0					652
Q4P3X7 UniProt NPD GO	BRE1_USTMA	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.92	-	nuc	0	Nucleus (By similarity)				817
P91133 UniProt NPD GO	UBR1_CAEEL	Ubiquitin-protein ligase E3 component N-recognin (EC 6.-.-.-) (Ubiquitin-protein ligase E3-alpha)	0.92	-	end	0					1927
Q9NTX9 UniProt NPD GO	CT177_HUMAN	Uncharacterized protein C20orf177	0.92	-	nuc	0					383
P40065 UniProt NPD GO	YET6_YEAST	Uncharacterized protein YER106W	0.92	-	nuc	0		condensed nuclear chromosome kinetochore [IDA]			302
Q06146 UniProt NPD GO	YL257_YEAST	Uncharacterized protein YLR257W	0.92	+	nuc	0	Cytoplasm	cytoplasm [IDA]			321
Q12276 UniProt NPD GO	YO227_YEAST	Uncharacterized protein YOR227W	0.92	-	nuc	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			1246
Q02749 UniProt NPD GO	YP068_YEAST	Uncharacterized protein YPL068C	0.92	+	nuc	0	Nucleus	nucleus [IDA]			293
Q06108 UniProt NPD GO	YP115_YEAST	Uncharacterized protein YPR115W	0.92	+	nuc	0	Cytoplasm	cytoplasm [IDA]			1083
P46939 UniProt NPD GO	UTRO_HUMAN	Utrophin (Dystrophin-related protein 1) (DRP1) (DRP)	0.92	-	nuc	0	Neuromuscular junction	cytoskeleton [TAS] membrane fraction [TAS] plasma membrane [TAS]	128240	1QAG	3433
Q8CGB3 UniProt NPD GO	UACA_MOUSE	Uveal autoantigen with coiled-coil domains and ankyrin repeats protein (Nucling) (Nuclear membrane-b ...	0.92	-	nuc	0	Nucleus. Cytoplasm. Expressed diffusely in cytoplasm	apoptosome [IDA] cytoplasm [IDA] cytosol [IDA] membrane fraction [IDA] nuclear envelope [IDA] nucleus [IDA] perinuclear region [IDA] soluble fraction [IDA]			1411
P34088 UniProt NPD GO	RAG1_RABIT	V(D)J recombination-activating protein 1 (RAG-1)	0.92	+	nuc	0	Nucleus				1042
Q9MYV3 UniProt NPD GO	VEGFA_CANFA	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.92	+	nuc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				214
P15692 UniProt NPD GO	VEGFA_HUMAN	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.92	+	nuc	0	Secreted protein. VEGF121 is acidic and freely secreted. VEGF165 is more basic, has heparin-binding ...	extracellular matrix (sensu Metazoa) [NAS] extracellular space [IDA]	192240	2VPF	232
Q9U8M0 UniProt NPD GO	VIT1_PERAM	Vitellogenin-1 precursor (Vg-1)	0.92	-	nuc	0	Secreted protein				1896
P02845 UniProt NPD GO	VIT2_CHICK	Vitellogenin-2 precursor (Vitellogenin II) (Major vitellogenin) [Contains: Lipovitellin-1 (Lipovitel ...	0.92	-	nuc	0					1850
Q8VGC3 UniProt NPD GO	CACB2_RAT	Voltage-dependent L-type calcium channel subunit beta-2 (CAB2) (Calcium channel voltage-dependent su ...	0.92	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side			1T0J	655
Q9H967 UniProt NPD GO	WDR76_HUMAN	WD repeat protein 76	0.92	-	nuc	0					626
Q9UPY6 UniProt NPD GO	WASF3_HUMAN	Wiskott-Aldrich syndrome protein family member 3 (WASP-family protein member 3) (Protein WAVE-3) (Ve ...	0.92	+	nuc	0	Cytoplasm		605068		502
P49750 UniProt NPD GO	YLPM1_HUMAN	YLP motif-containing protein 1 (Nuclear protein ZAP3) (ZAP113)	0.92	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				1951
O75152 UniProt NPD GO	ZC11A_HUMAN	Zinc finger CCCH domain-containing protein 11A	0.92	-	nuc	0					810
Q9UPT8 UniProt NPD GO	CS007_HUMAN	Zinc finger CCCH domain-containing protein C19orf7	0.92	+	nuc	0				2CQE	1303
Q6ZPZ3 UniProt NPD GO	CS007_MOUSE	Zinc finger CCCH domain-containing protein C19orf7 homolog	0.92	+	nuc	0					1304
Q7Z2W4 UniProt NPD GO	ZCC2_HUMAN	Zinc finger CCCH type antiviral protein 1 (Zinc finger CCCH domain-containing protein 2)	0.92	-	nuc	0	Nucleus (Potential)		607312		902
Q69ZB8 UniProt NPD GO	ZCHC2_MOUSE	Zinc finger CCHC domain-containing protein 2 (Fragment)	0.92	-	nuc	0					1168
Q9Y3M9 UniProt NPD GO	ZN337_HUMAN	Zinc finger protein 337	0.92	-	nuc	0	Nucleus (Probable)				751
Q8N184 UniProt NPD GO	ZN567_HUMAN	Zinc finger protein 567	0.92	-	nuc	0	Nucleus (Potential)				616
Q96N20 UniProt NPD GO	ZN75A_HUMAN	Zinc finger protein 75A	0.92	+	nuc	0	Nucleus (Potential)		601473		296
P34706 UniProt NPD GO	SDC3_CAEEL	Zinc finger protein sdc-3	0.92	+	nuc	0	Nucleus	nucleus [IDA]			2150
Q8R515 UniProt NPD GO	ZHX1_RAT	Zinc fingers and homeoboxes protein 1	0.92	+	exc	0	Nucleus	nucleus [IDA]			873
Q8K1L0 UniProt NPD GO	CREB5_MOUSE	cAMP response element-binding protein 5 (CRE-BPa) (Fragment)	0.92	+	nuc	0	Nucleus (Probable)	nucleus [ISS]			353
Q9UJA5 UniProt NPD GO	TRM6_HUMAN	tRNA (adenine-N(1)-)-methyltransferase non-catalytic subunit TRM6 (tRNA(m1A58)-methyltransferase sub ...	0.92	-	nuc	0	Nucleus (By similarity)				497
O20163 UniProt NPD GO	TILS_CHLVU	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.92	-	nuc	1 *	Plastid; chloroplast				504
O23826 UniProt NPD GO	K125_TOBAC	125 kDa kinesin-related protein	0.91	-	nuc	0	Cytoplasm. Microtubule-associated				1006
Q9QWY8 UniProt NPD GO	DDEF1_MOUSE	130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein (PIP2-dependen ...	0.91	-	nuc	0	Cytoplasm. Predominantly. Membrane. Partially membrane-associated				1147
Q61733 UniProt NPD GO	RT31_MOUSE	28S ribosomal protein S31, mitochondrial precursor (S31mt) (MRP-S31) (Imogen 38)	0.91	-	nuc	0	Mitochondrion (By similarity)	mitochondrion [IDA]			384
O01727 UniProt NPD GO	RS6_BRAFL	40S ribosomal protein S6	0.91	+	nuc	0					244
P22147 UniProt NPD GO	XRN1_YEAST	5'-3' exoribonuclease 1 (EC 3.1.11.-) (Strand exchange protein 1) (KAR(-)-enhancing mutation protein ...	0.91	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Predominantly cytoplasmic, also perinuclear	cytoplasm [TAS] cytoplasmic mRNA processing body [IDA]			1528

You are viewing entries 3551 to 3600 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.