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
Q13522 UniProt NPD GO	IPP1_HUMAN	Protein phosphatase inhibitor 1 (IPP-1) (I-1)	0.84	-	nuc	0					171
P01099 UniProt NPD GO	IPP1_RABIT	Protein phosphatase inhibitor 1 (IPP-1) (I-1)	0.84	-	nuc	0					166
P21520 UniProt NPD GO	SCA_DROME	Protein scabrous precursor	0.84	-	nuc	1 *	Endosome; late endosome. Colocalizes in late endosomes with Gp150	extracellular region [NAS]			799
P16879 UniProt NPD GO	FES_MOUSE	Proto-oncogene tyrosine-protein kinase Fes/Fps (EC 2.7.10.2) (C-Fes)	0.84	-	nuc	0					820
Q92347 UniProt NPD GO	YDH2_SCHPO	Pumilio domain-containing protein C6G9.02c	0.84	-	mit	0					655
Q9FVV4 UniProt NPD GO	RH55_ARATH	Putative DEAD-box ATP-dependent RNA helicase 55 (EC 3.6.1.-)	0.84	+	mit	0					465
Q9SZI6 UniProt NPD GO	GAT20_ARATH	Putative GATA transcription factor 20	0.84	-	nuc	0	Nucleus (Probable)				352
Q09818 UniProt NPD GO	YAC4_SCHPO	Putative general negative regulator of transcription C16C9.04c	0.84	+	nuc	0	Nucleus (Probable)				489
Q8N428 UniProt NPD GO	GLTL1_HUMAN	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 1 (EC 2.4.1.41) (Protein-UDP ace ...	0.84	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				558
Q9JJ61 UniProt NPD GO	GLTL1_MOUSE	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 1 (EC 2.4.1.41) (Protein-UDP ace ...	0.84	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				558
P40657 UniProt NPD GO	SOX15_DROME	Putative transcription factor SOX-15 (Sox50E)	0.84	+	nuc	0	Nucleus (Potential)				784
Q6UXX9 UniProt NPD GO	RSPO2_HUMAN	R-spondin-2 precursor (Roof plate-specific spondin-2) (hRspo2)	0.84	+	nuc	0	Secreted protein (By similarity)				243
Q8TDY2 UniProt NPD GO	RBCC1_HUMAN	RB1-inducible coiled-coil protein 1	0.84	-	nuc	0	Nucleus		606837		1594
Q8CFE3 UniProt NPD GO	RCOR1_MOUSE	REST corepressor 1 (Protein CoREST)	0.84	+	nuc	0	Nucleus (By similarity)				477
Q6P116 UniProt NPD GO	RCOR2_BRARE	REST corepressor 2	0.84	-	nuc	0	Nucleus (By similarity)				536
O15034 UniProt NPD GO	RIMB2_HUMAN	RIM-binding protein 2 (RIM-BP2)	0.84	-	nuc	0	Synaptic plasma membrane (By similarity)			2CSQ	1052
Q5XF85 UniProt NPD GO	ATL4J_ARATH	RING-H2 finger protein ATL4J precursor	0.84	-	exc	1 *					432
Q9BVN2 UniProt NPD GO	RUSC1_HUMAN	RUN and SH3 domain-containing protein 1 (New molecule containing SH3 at the carboxy-terminus) (Nesca ...	0.84	-	nuc	0	Cytoplasm. Nucleus. Translocated to the nuclear envelope upon stimulation with NGF				902
Q63713 UniProt NPD GO	RASA2_RAT	Ras GTPase-activating protein 2 (GAP1m)	0.84	-	nuc	0	Cell membrane (Potential)				847
Q6XUX2 UniProt NPD GO	RIPK5_RAT	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.84	-	cyt	0	Cytoplasm (Probable)				927
Q67E00 UniProt NPD GO	RIPK5_XENTR	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.84	+	nuc	0	Cytoplasm (Probable)				918
O14924 UniProt NPD GO	RGS12_HUMAN	Regulator of G-protein signaling 12 (RGS12)	0.84	-	nuc	0	Nucleus	condensed nuclear chromosome [TAS]	602512		1447
P11416 UniProt NPD GO	RARA_MOUSE	Retinoic acid receptor alpha (RAR-alpha)	0.84	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			462
P18514 UniProt NPD GO	RARA_NOTVI	Retinoic acid receptor alpha (RAR-alpha)	0.84	+	nuc	0	Nucleus				458
Q91392 UniProt NPD GO	RARG_BRARE	Retinoic acid receptor gamma (RAR-gamma) (ZRAR gamma)	0.84	+	nuc	0	Nucleus				499
Q92888 UniProt NPD GO	ARHG1_HUMAN	Rho guanine nucleotide exchange factor 1 (p115-RhoGEF) (p115RhoGEF) (115 kDa guanine nucleotide exch ...	0.84	-	nuc	0	Cytoplasm. Membrane. Translocated to the membrane by activated GNA13 or LPA stimulation	cytoplasm [TAS] plasma membrane [TAS]	601855	1SHZ	912
Q09697 UniProt NPD GO	RGA8_SCHPO	Rho-GTPase-activating protein 8	0.84	-	nuc	0	Cytoplasm. Localizes to the cell ends during interphase and to the septum-forming region during cyto ...	cell cortex of cell tip [IDA] medial ring [IDA]			777
P61584 UniProt NPD GO	ROCK1_PANTR	Rho-associated protein kinase 1 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.84	-	nuc	0	Cytoplasm. Associated with the mother centriole and an intercentriolar linker. Golgi apparatus; Golg ...				1003
O77819 UniProt NPD GO	ROCK1_RABIT	Rho-associated protein kinase 1 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.84	-	nuc	0	Cytoplasm. Associated with the mother centriole and an intercentriolar linker. Golgi apparatus; Golg ...				1354
Q63644 UniProt NPD GO	ROCK1_RAT	Rho-associated protein kinase 1 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.84	-	nuc	0	Cytoplasm. Associated with the mother centriole and an intercentriolar linker. Golgi apparatus; Golg ...				1369
Q5R7B0 UniProt NPD GO	RPP29_PONPY	Ribonuclease P protein subunit p29 (EC 3.1.26.5)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				220
Q92562 UniProt NPD GO	SAC3_HUMAN	SAC domain-containing protein 3	0.84	-	cyt	0			609390		907
Q922D4 UniProt NPD GO	SAPS3_MOUSE	SAPS domain family member 3	0.84	-	nuc	0					844
Q80VA5 UniProt NPD GO	S3TC2_MOUSE	SH3 domain and tetratricopeptide repeats-containing protein 2	0.84	-	cyt	0					1289
Q9UTN6 UniProt NPD GO	SNF21_SCHPO	SNF2-family ATP-dependent chromatin remodeling factor snf21 (EC 3.6.1.-) (ATP-dependent helicase snf ...	0.84	-	nuc	0	Nucleus (Potential)				1199
P27609 UniProt NPD GO	HMEN_BOMMO	Segmentation polarity homeobox protein engrailed	0.84	+	nuc	0	Nucleus (Potential)				372
Q5U7M9 UniProt NPD GO	SEMG2_MACNE	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.84	-	nuc	0	Secreted protein (By similarity)				582
Q14674 UniProt NPD GO	ESPL1_HUMAN	Separin (EC 3.4.22.49) (Separase) (Caspase-like protein ESPL1) (Extra spindle poles-like 1 protein)	0.84	-	end	0	Cytoplasm. Nucleus	centrosome [IEP]	604143		2120
P33122 UniProt NPD GO	TYE7_YEAST	Serine-rich protein TYE7 (Basic-helix-loop-helix protein SGC1)	0.84	-	nuc	0	Nucleus (Probable)	nucleus [IC]			291
Q5K8D3 UniProt NPD GO	ATG1_CRYNE	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.84	-	nuc	0	Cytoplasm (By similarity)				988
P53104 UniProt NPD GO	ATG1_YEAST	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1) (Autophagy protein ...	0.84	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in pre-autophagosomal structure and other pu ...	cytosol [IDA]			897
Q6TGC6 UniProt NPD GO	CBK1_PNECA	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1)	0.84	-	cyt	0					507
Q75DB8 UniProt NPD GO	ATR_ASHGO	Serine/threonine-protein kinase MEC1 (EC 2.7.11.1) (DNA-damage checkpoint kinase MEC1) (Mitosis entr ...	0.84	-	end	0	Nucleus. Localizes to nuclear DNA repair foci in response to DNA double strand breaks (By similarity ...				2324
Q6DT37 UniProt NPD GO	MRCKG_HUMAN	Serine/threonine-protein kinase MRCK gamma (EC 2.7.11.1) (CDC42-binding protein kinase gamma) (Myoto ...	0.84	-	nuc	0	Cytoplasm. Concentrates at the leading edge of cells	leading edge [IDA]			1551
Q61036 UniProt NPD GO	PAK3_MOUSE	Serine/threonine-protein kinase PAK 3 (EC 2.7.11.1) (p21-activated kinase 3) (PAK-3) (Beta-PAK) (CDC ...	0.84	-	nuc	0				1EES	559
Q6FRZ9 UniProt NPD GO	ATM_CANGA	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.84	-	nuc	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2763
O35385 UniProt NPD GO	PPE2_MOUSE	Serine/threonine-protein phosphatase with EF-hands 2 (EC 3.1.3.16) (PPEF-2)	0.84	-	cyt	0					757
Q8CCP0 UniProt NPD GO	SDCG1_MOUSE	Serologically defined colon cancer antigen 1	0.84	-	nuc	0	Nucleus (Potential)				1064
O60524 UniProt NPD GO	SDCG1_HUMAN	Serologically defined colon cancer antigen 1 (Antigen NY-CO-1)	0.84	-	nuc	0	Nucleus (Potential)		608378		1076
Q864Q1 UniProt NPD GO	SRY_NEOPH	Sex-determining region Y protein (Testis-determining factor)	0.84	+	nuc	0	Nucleus				196

You are viewing entries 7151 to 7200 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.