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
O93262 UniProt NPD GO	SOML_ACITR	Somatolactin precursor (SL)	0.17	-	exc	0	Secreted protein				232
P30872 UniProt NPD GO	SSR1_HUMAN	Somatostatin receptor type 1 (SS1R) (SRIF-2)	0.17	-	vac	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	182451		391
P30873 UniProt NPD GO	SSR1_MOUSE	Somatostatin receptor type 1 (SS1R) (SRIF-2)	0.17	-	vac	7	Membrane; multi-pass membrane protein	membrane fraction [IDA] plasma membrane [IDA]			391
P28646 UniProt NPD GO	SSR1_RAT	Somatostatin receptor type 1 (SS1R) (SRIF-2)	0.17	-	vac	7	Membrane; multi-pass membrane protein				391
Q64256 UniProt NPD GO	HSP3_RAT	Sperm protamine P3	0.17	-	nuc	0	Nucleus (By similarity)				104
P26461 UniProt NPD GO	IACS_PIG	Sperm-associated acrosin inhibitor precursor (AI)	0.17	-	exc	0	Secreted protein				97
Q5R997 UniProt NPD GO	SPIN1_PONPY	Spindlin-1	0.17	-	mit	0	Nucleus (By similarity)				262
Q4V8J7 UniProt NPD GO	SPIN1_RAT	Spindlin-1	0.17	-	mit	0	Nucleus (By similarity)				262
Q61142 UniProt NPD GO	SPIN1_MOUSE	Spindlin-1 (30000 Mr metaphase complex) (SSEC P)	0.17	-	mit	0	Nucleus. Associates with the meiotic spindle	spindle [IDA]			262
Q9Y657 UniProt NPD GO	SPIN1_HUMAN	Spindlin-1 (Ovarian cancer-related protein)	0.17	-	mit	0	Nucleus		609936		262
Q99865 UniProt NPD GO	SPIN3_HUMAN	Spindlin-3 (Spindlin-like protein 3) (SPIN-3) (Protein DXF34)	0.17	-	cyt	0					258
Q752X9 UniProt NPD GO	FDFT_ASHGO	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.17	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				441
P08842 UniProt NPD GO	STS_HUMAN	Steryl-sulfatase precursor (EC 3.1.6.2) (Steroid sulfatase) (Steryl-sulfate sulfohydrolase) (Arylsul ...	0.17	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] endosome [TAS] Golgi apparatus [TAS] lysosome [TAS] membrane fraction [TAS] microsome [TAS] plasma membrane [TAS]	308100	1P49	583
P15004 UniProt NPD GO	PER2_LYCES	Suberization-associated anionic peroxidase 2 precursor (EC 1.11.1.7) (TMP2)	0.17	-	exc	1 *	Secreted protein (By similarity)				363
Q99954 UniProt NPD GO	SMR3A_HUMAN	Submaxillary gland androgen-regulated protein 3 homolog A precursor (Proline-rich protein 5) (Prolin ...	0.17	-	exc	0	Secreted protein (Potential)	extracellular region [TAS]			134
Q9G4F5 UniProt NPD GO	CYSA_CUCSA	Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase)	0.17	-	cyt	0	Mitochondrion (Potential)				350
Q9Y6N5 UniProt NPD GO	SQRD_HUMAN	Sulfide:quinone oxidoreductase, mitochondrial precursor (EC 1.-.-.-)	0.17	-	cyt	0	Mitochondrion (Probable)				450
O46503 UniProt NPD GO	ST1C1_RABIT	Sulfotransferase 1C1 (EC 2.8.2.-) (rabSULT1C2)	0.17	-	nuc	0	Cytoplasm				296
Q9QWG7 UniProt NPD GO	ST1B1_MOUSE	Sulfotransferase family cytosolic 1B member 1 (EC 2.8.2.-) (Sulfotransferase 1B1) (DOPA/tyrosine sul ...	0.17	-	cyt	0	Cytoplasm (By similarity)	cytosol [TAS]			299
P38751 UniProt NPD GO	SHU1_YEAST	Suppressor of HU sensitivity involved in recombination protein 1	0.17	-	cyt	0		nucleus [IDA]			150
P15799 UniProt NPD GO	C170_GIALA	Surface antigen CRP170 (Fragment)	0.17	-	nuc	0					328
Q92356 UniProt NPD GO	SYB1_SCHPO	Synaptobrevin homolog 1	0.17	-	nuc	1	Membrane; single-pass type IV membrane protein. Accumulates in vesicle-like structures at the medial ...	cell cortex of cell tip [IDA] cytoplasmic vesicle membrane [IDA] medial ring [IDA]			121
Q6DRJ9 UniProt NPD GO	RIC8B_BRARE	Synembryn-B (Protein Ric-8B) (Synembryn-like)	0.17	-	cyt	0	Cytoplasm (By similarity)				536
Q95LI7 UniProt NPD GO	CD3G_MACFA	T-cell surface glycoprotein CD3 gamma chain precursor (T-cell receptor T3 gamma chain)	0.17	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] T cell receptor complex [ISS]			181
P31043 UniProt NPD GO	CD28_CHICK	T-cell-specific surface glycoprotein CD28 homolog precursor (CHT28)	0.17	-	nuc	1	Membrane; single-pass type I membrane protein				221
P40413 UniProt NPD GO	TCPE_YEAST	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.17	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IPI] cytoplasm [TAS] cytoskeleton [TAS]			551
Q5RCD2 UniProt NPD GO	TCPZ_PONPY	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta)	0.17	-	cyt	0	Cytoplasm (By similarity)				530
P40227 UniProt NPD GO	TCPZ_HUMAN	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta) (CCT-zeta-1) (Tcp20) (HTR3) (Acute morphine ...	0.17	-	cyt	0	Cytoplasm	cytoplasm [TAS]	104613		530
Q9JJ78 UniProt NPD GO	TOPK_MOUSE	T-lymphokine-activated killer cell-originated protein kinase (EC 2.7.12.2) (T-LAK cell-originated pr ...	0.17	-	nuc	0					330
P56840 UniProt NPD GO	TCLB1_MOUSE	TCL1B1 protein	0.17	-	cyt	0					116
P56842 UniProt NPD GO	TCLB3_MOUSE	TCL1B3 protein	0.17	-	cyt	0					122
P56844 UniProt NPD GO	TCLB4_MOUSE	TCL1B4 protein	0.17	-	cyt	0					120
O95411 UniProt NPD GO	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1 (12 kDa TGF-beta1-induced antiapoptotic factor)	0.17	-	nuc	0	Nucleus	nucleus [NAS]			115
Q9Z1S4 UniProt NPD GO	TIAF1_MOUSE	TGFB1-induced anti-apoptotic factor 1 (12 kDa TGF-beta1-induced antiapoptotic factor)	0.17	-	nuc	0	Nucleus				115
P25638 UniProt NPD GO	TAH1_YEAST	TPR repeat-containing protein associated with Hsp9P25638part1	0.17	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			111
Q5TJE4 UniProt NPD GO	TPSN_CANFA	Tapasin precursor (TPSN) (TPN) (TAP-binding protein)	0.17	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				449
Q646A3 UniProt NPD GO	TA2R8_GORGO	Taste receptor type 2 member 1 (T2R8)	0.17	-	end	7 *	Membrane; multi-pass membrane protein				309
Q645Y7 UniProt NPD GO	T2R39_GORGO	Taste receptor type 2 member 39 (T2R39)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				338
P59534 UniProt NPD GO	T2R39_HUMAN	Taste receptor type 2 member 39 (T2R39) (T2R57)	0.17	-	end	6 *	Membrane; multi-pass membrane protein				338
P69764 UniProt NPD GO	CXT5A_CONMR	Tau conotoxin mr5a precursor	0.17	-	exc	0	Secreted protein				59
Q2QLA1 UniProt NPD GO	TES_MONDO	Testin	0.17	-	nuc	0					422
O08716 UniProt NPD GO	TLBP_MOUSE	Testis lipid-binding protein (TLBP) (15 kDa perforatorial protein) (PERF 15)	0.17	-	cyt	0	Cytoplasm (Potential)				132
Q85G31 UniProt NPD GO	THIG_CYAME	Thiazole biosynthesis protein thiG	0.17	-	mit	0	Plastid; chloroplast				258
P23618 UniProt NPD GO	THI4_FUSOX	Thiazole biosynthetic enzyme, mitochondrial precursor (Stress-inducible protein sti35)	0.17	-	mit	0	Mitochondrion (Potential)				320
Q05895 UniProt NPD GO	TSP3_MOUSE	Thrombospondin-3 precursor	0.17	-	nuc	0					956
Q8JGW0 UniProt NPD GO	TSP4_BRARE	Thrombospondin-4 precursor (Thbs4)	0.17	-	vac	0		extracellular region [NAS]			949
O62643 UniProt NPD GO	THY1_MACMU	Thy-1 membrane glycoprotein precursor (Thy-1 antigen) (CD90 antigen) (CDw90 antigen)	0.17	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cytosol [ISS] external side of plasma membrane [ISS] growth cone [ISS] lipid raft [ISS] plasma membrane [ISS]			161
P36590 UniProt NPD GO	KTHY_SCHPO	Thymidylate kinase (EC 2.7.4.9) (dTMP kinase)	0.17	-	cyt	0					210
Q95NU5 UniProt NPD GO	TORS_CAEEL	Torsin-like protein precursor (Abnormal oocyte formation protein 5)	0.17	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen				356
P58762 UniProt NPD GO	CTXA_CHIQU	Toxin A precursor (CqTX-A)	0.17	-	exc	1 *	Secreted protein. Found in nematocyst				462

You are viewing entries 55001 to 55050 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.