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
Q9M841 UniProt NPD GO	PEX12_ARATH	Putative peroxisome assembly protein 12 (Peroxin-12)	0.57	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (Potential)				372
P83099 UniProt NPD GO	KPC4_DROME	Putative protein kinase C, delta type homolog (EC 2.7.11.13)	0.57	-	mit	0					671
P25602 UniProt NPD GO	YCH6_YEAST	Putative uncharacterized protein YCL076W	0.57	+	nuc	0					247
P34303 UniProt NPD GO	YKQ8_CAEEL	Putative zinc finger protein C06E1.8	0.57	-	nuc	0	Nucleus (Potential)				397
Q04781 UniProt NPD GO	YM81_YEAST	RING finger protein YMR247C	0.57	-	nuc	0					1562
Q8LFY8 UniProt NPD GO	ATL1O_ARATH	RING-H2 finger protein ATL1O (RING-H2 finger protein ATL11)	0.57	-	nuc	1					413
O14227 UniProt NPD GO	RDR1_SCHPO	RNA-dependent RNA polymerase homolog 1 (Protein rdp1)	0.57	-	nuc	0		centric heterochromatin [IDA] mating-type region heterochromatin [IDA] nuclear RNA-directed RNA polymerase complex [IDA] nuclear telomeric heterochromatin [IDA] nucleus [IDA]			1215
Q96NA2 UniProt NPD GO	RILP_HUMAN	Rab-interacting lysosomal protein	0.57	-	nuc	0	Intracytoplasmic membrane. Endosome; late endosome; late endosomal membrane. Lysosome; lysosomal mem ...		607848	1YHN	401
Q80UJ7 UniProt NPD GO	RB3GP_MOUSE	Rab3 GTPase-activating protein catalytic subunit (RAB3 GTPase-activating protein 130 kDa subunit) (R ...	0.57	-	cyt	0	Cytoplasm (By similarity). In neurons, it is enriched in the synaptic soluble fraction (By similarit ...				980
Q99NF8 UniProt NPD GO	RBP17_MOUSE	Ran-binding protein 17	0.57	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus; nuclear envelope; nuclear pore complex ...				1088
Q86VI3 UniProt NPD GO	IQGA3_HUMAN	Ras GTPase-activating-like protein IQGAP3	0.57	-	mit	0					1631
Q9ER80 UniProt NPD GO	RTP4_MOUSE	Receptor-transporting protein 4 (28 kDa interferon-responsive protein)	0.57	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)				249
P58751 UniProt NPD GO	RELN_RAT	Reelin precursor (EC 3.4.21.-)	0.57	-	nuc	1 *	Secreted protein (By similarity)				3462
Q80U57 UniProt NPD GO	RIMS3_MOUSE	Regulating synaptic membrane exocytosis protein 3 (Nim3) (Rab-3-interacting molecule 3) (RIM 3) (RIM ...	0.57	-	nuc	0					307
O08849 UniProt NPD GO	RGS2_MOUSE	Regulator of G-protein signaling 2 (RGS2)	0.57	-	nuc	0		nucleus [TAS]			211
Q5DRQ5 UniProt NPD GO	RTBDN_SPETR	Retbindin precursor	0.57	-	nuc	0	Secreted protein (Potential)				254
Q91WE3 UniProt NPD GO	RPP25_MOUSE	Ribonuclease P protein subunit p25 (EC 3.1.26.5) (RNase P protein subunit p25)	0.57	-	nuc	0	Nucleus (By similarity)				199
Q5PPN2 UniProt NPD GO	RPP25_RAT	Ribonuclease P protein subunit p25 (EC 3.1.26.5) (RNase P protein subunit p25)	0.57	-	nuc	0	Nucleus (By similarity)				199
Q05942 UniProt NPD GO	RSA3_YEAST	Ribosome assembly protein 3	0.57	+	nuc	0	Nucleus; nucleolus	nucleolar preribosome, large subunit precursor [IDA] nucleolus [IDA]			220
Q14137 UniProt NPD GO	BOP1_HUMAN	Ribosome biogenesis protein BOP1 (Block of proliferation 1 protein)	0.57	-	mit	0	Nucleus; nucleolus				746
Q6CF69 UniProt NPD GO	RLP24_YARLI	Ribosome biogenesis protein RLP24	0.57	-	nuc	0	Nucleus; nucleolus (By similarity)				188
Q9LQ89 UniProt NPD GO	ROGF2_ARATH	Rop guanine nucleotide exchange factor 2 (RopGEF2)	0.57	-	nuc	0					516
P11716 UniProt NPD GO	RYR1_RABIT	Ryanodine receptor 1 (Skeletal muscle-type ryanodine receptor) (RyR1) (RYR-1) (Skeletal muscle calci ...	0.57	+	end	6	Membrane; multi-pass membrane protein (Potential)				5037
Q9UJW9 UniProt NPD GO	SRTD3_HUMAN	SERTA domain-containing protein 3 (Replication protein-binding trans-activator) (RPA-binding trans-a ...	0.57	-	nuc	0	Nucleus				196
P24054 UniProt NPD GO	SPRL1_RAT	SPARC-like protein 1 precursor (Matrix glycoprotein Sc1)	0.57	-	exc	0	Secreted protein; extracellular space; extracellular matrix	synapse [IDA]			634
P38326 UniProt NPD GO	SWC5_YEAST	SWR1-complex protein 5	0.57	-	nuc	0	Nucleus	nucleus [IDA] SWR1 complex [IPI]			303
Q9Z1N6 UniProt NPD GO	SFRP4_MOUSE	Secreted frizzled-related sequence protein 4 precursor (sFRP-4) (Frizzled-related protein 4) (FRP-4) ...	0.57	-	mit	0	Secreted protein (By similarity)				351
P04279 UniProt NPD GO	SEMG1_HUMAN	Semenogelin-1 precursor (Semenogelin I) (SGI) [Contains: Alpha-inhibin-92; Alpha-inhibin-31; Seminal ...	0.57	-	nuc	0	Secreted protein	extracellular space [TAS]	182140		462
P48009 UniProt NPD GO	SPN4_SCHPO	Septin homolog spn4	0.57	-	cyt	0		septin complex [IDA] septin ring (sensu Fungi) [IDA]			380
Q9NVA2 UniProt NPD GO	SEP11_HUMAN	Septin-11	0.57	-	nuc	0		stress fiber [IDA]			428
Q60806 UniProt NPD GO	PLK3_MOUSE	Serine/threonine-protein kinase PLK3 (EC 2.7.11.21) (Polo-like kinase 3) (PLK-3) (Cytokine-inducible ...	0.57	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				631
Q9S713 UniProt NPD GO	STT7_ARATH	Serine/threonine-protein kinase SNT7, chloroplast precursor (EC 2.7.11.1) (Stt7 homolog)	0.57	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane	chloroplast [IDA]			562
O13310 UniProt NPD GO	ORB6_SCHPO	Serine/threonine-protein kinase orb6 (EC 2.7.11.1)	0.57	-	cyt	0		cell cortex of cell tip [IDA]			469
P11831 UniProt NPD GO	SRF_HUMAN	Serum response factor (SRF)	0.57	-	nuc	0	Nucleus	nucleus [TAS]	600589	1SRS	508
Q9JM73 UniProt NPD GO	SRF_MOUSE	Serum response factor (SRF)	0.57	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			504
Q9SE35 UniProt NPD GO	SIL1_CYLFU	Silaffin 1 precursor (natSil-1) [Contains: Silaffin-1B; Silaffin-1A2; Silaffin-1A1]	0.57	-	exc	0					265
Q99250 UniProt NPD GO	SCN2A_HUMAN	Sodium channel protein type 2 subunit alpha (Sodium channel protein type II subunit alpha) (Voltage- ...	0.57	+	end	17	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601219		2005
P50482 UniProt NPD GO	SL9A2_RABIT	Sodium/hydrogen exchanger 2 (Na(+)/H(+) exchanger 2) (NHE-2) (Solute carrier family 9 member 2)	0.57	-	end	12 *	Membrane; multi-pass membrane protein				809
O88307 UniProt NPD GO	SORL_MOUSE	Sortilin-related receptor precursor (Sorting protein-related receptor containing LDLR class A repeat ...	0.57	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				2215
P11474 UniProt NPD GO	ERR1_HUMAN	Steroid hormone receptor ERR1 (Estrogen-related receptor, alpha) (ERR-alpha) (Estrogen receptor-like ...	0.57	-	cyt	0	Nucleus	nucleus [TAS]	601998	1XB7	519
Q04752 UniProt NPD GO	STF1_BOVIN	Steroidogenic factor 1 (STF-1) (SF-1) (Adrenal 4-binding protein) (Steroid hormone receptor Ad4BP) ( ...	0.57	+	mit	0	Nucleus	nucleus [IMP]			461
P32420 UniProt NPD GO	DHSB_USTMA	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.57	-	mit	0	Mitochondrion; mitochondrial inner membrane				295
P57075 UniProt NPD GO	STS2_HUMAN	Suppressor of T-cell receptor signaling 2 (STS-2) (Cbl-interacting protein 4) (CLIP4) (T-cell ubiqui ...	0.57	-	nuc	0	Cytoplasm. Nucleus		605736	2CRN	661
O02771 UniProt NPD GO	SMN_CANFA	Survival motor neuron protein	0.57	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in subnuclear structures next to coile ...				287
O42260 UniProt NPD GO	GEMI2_XENLA	Survival of motor neuron protein-interacting protein 1 (SMN-interacting protein 1) (Component of gem ...	0.57	-	nuc	0	Nucleus; gem. Localized in subnuclear structures next to coiled bodies, called gems, which are highl ...				259
Q64332 UniProt NPD GO	SYN2_MOUSE	Synapsin-2 (Synapsin II)	0.57	-	nuc	0	Synapse	synapse [IDA] synaptic vesicle membrane [IDA]			586
Q9R0N4 UniProt NPD GO	SYT10_MOUSE	Synaptotagmin-10 (Synaptotagmin X) (SytX)	0.57	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				523
Q16932 UniProt NPD GO	STX_APLCA	Syntaxin	0.57	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				290
Q5REB4 UniProt NPD GO	STX18_PONPY	Syntaxin-18	0.57	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				335
Q9LK09 UniProt NPD GO	SYP32_ARATH	Syntaxin-32 (AtSYP32)	0.57	-	nuc	1	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type IV membrane protein ...				347

You are viewing entries 21001 to 21050 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.