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
Q25520 UniProt NPD GO	RUNT_MANSE	Segmentation protein Runt (Fragment)	0.00	-	cyt	0	Nucleus (By similarity)				79
Q9VMV6 UniProt NPD GO	SELT_DROME	SelT-like protein precursor	0.00	-	end	3 *					198
Q28920 UniProt NPD GO	SPMI_PIG	Seminal plasma sperm motility inhibitor precursor	0.00	-	exc	0	Secreted protein				137
P08819 UniProt NPD GO	CBP2_WHEAT	Serine carboxypeptidase 2 (EC 3.4.16.6) (Serine carboxypeptidase II) (Carboxypeptidase D) (CPDW-II) ...	0.00	-	cyt	0				3SC2	423
P17207 UniProt NPD GO	SER3_DROME	Serine protease 3 precursor (EC 3.4.21.-) (Protein Jonah 99Ci)	0.00	-	exc	0					272
P58516 UniProt NPD GO	SPI3_SOLTU	Serine protease inhibitor 3 (PSPI-22) (Fragment)	0.00	-	cyt	0	Vacuole (By similarity)				21
Q30HU9 UniProt NPD GO	SPI1_CRAVI	Serine protease inhibitor Cvsi-1 precursor	0.00	-	exc	0	Secreted protein				90
P17205 UniProt NPD GO	SER1_DROME	Serine proteases 1/2 precursor (EC 3.4.21.-) (Protein Jonah 99Cii/99Ciii)	0.00	-	exc	0					265
Q10997 UniProt NPD GO	SPI_HALRO	Serine proteinase inhibitor (Fragment)	0.00	-		0					10
Q7M4T6 UniProt NPD GO	PIA1_PLEOS	Serine proteinase inhibitor IA-1 (Proteinase A inhibitor 1)	0.00	-	nuc	0				1V5I	76
Q7M4T5 UniProt NPD GO	PIA2_PLEOS	Serine proteinase inhibitor IA-2 (Proteinase A inhibitor 2)	0.00	-	cyt	0					76
Q8AX00 UniProt NPD GO	MOS_SIBNE	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.00	-	exc	0					193
P20604 UniProt NPD GO	PP11_YEAST	Serine/threonine-protein phosphatase PP1-1 (EC 3.1.3.16)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			311
P38924 UniProt NPD GO	PAU1_YEAST	Seripauperin-1/14	0.00	-	exc	0					120
P53343 UniProt NPD GO	PAU12_YEAST	Seripauperin-12	0.00	-	exc	0					120
P38725 UniProt NPD GO	PAU13_YEAST	Seripauperin-13 precursor	0.00	-	exc	0					120
P35994 UniProt NPD GO	PAU16_YEAST	Seripauperin-16 precursor	0.00	-	cyt	0					123
P32612 UniProt NPD GO	PAU2_YEAST	Seripauperin-2	0.00	-	exc	0					120
Q08322 UniProt NPD GO	PAU20_YEAST	Seripauperin-20	0.00	-	cyt	0	Membrane; single-pass membrane protein (Potential)				120
P53427 UniProt NPD GO	PAU4_YEAST	Seripauperin-4	0.00	-	exc	0					120
P43575 UniProt NPD GO	PAU5_YEAST	Seripauperin-5	0.00	-	cyt	0					122
P52921 UniProt NPD GO	PAU6_YEAST	Seripauperin-6/18	0.00	-	exc	0					120
P39545 UniProt NPD GO	PAU7_YEAST	Seripauperin-7	0.00	-	cyt	1 *					55
P53055 UniProt NPD GO	PAU8_YEAST	Seripauperin-8	0.00	-	exc	0					120
P42995 UniProt NPD GO	OXYT_BUFRE	Seritocin ([Ser5,Ile8]-oxytocin)	0.00	-		0	Secreted protein				9
P34571 UniProt NPD GO	SRT55_CAEEL	Serpentine receptor class T-55 precursor (Protein srt-55)	0.00	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				363
P83260 UniProt NPD GO	SRB8_CAEEL	Serpentine receptor class beta-8/9 (Protein srb-8/Srb-9)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				351
O17956 UniProt NPD GO	SRD28_CAEEL	Serpentine receptor class delta-28 (Protein srd-28)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				320
P19095 UniProt NPD GO	SAMP_MUSCA	Serum amyloid P-component (SAP) (Fragment)	0.00	-		0	Secreted protein				9
P20677 UniProt NPD GO	SAMP_PLEPL	Serum amyloid P-component (SAP) (Fragment)	0.00	-		0	Secreted protein				20
P07629 UniProt NPD GO	SAMP_MESAU	Serum amyloid P-component precursor (Female protein) (FP) (SAP(FP))	0.00	-	exc	0	Secreted protein			1HAS	234
P49255 UniProt NPD GO	SAMP_CAVPO	Serum amyloid P-component precursor (SAP)	0.00	-	vac	0	Secreted protein				223
P02743 UniProt NPD GO	SAMP_HUMAN	Serum amyloid P-component precursor (SAP) (9.5S alpha-1-glycoprotein) [Contains: Serum amyloid P-com ...	0.00	-	vac	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	104770	2A3Y	223
Q62086 UniProt NPD GO	PON2_MOUSE	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.00	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				354
Q9BGN0 UniProt NPD GO	PON3_RABIT	Serum paraoxonase/lactonase 3 (EC 3.1.1.-)	0.00	-	exc	0	Secreted protein; extracellular space (By similarity)				354
P13642 UniProt NPD GO	SYS_RABIT	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS) (62 kDa RNA-binding protein) (Frag ...	0.00	-	cyt	0					39
P84868 UniProt NPD GO	SESQN_VIGUS	Sesquin (Fragment)	0.00	-		0					10
P84632 UniProt NPD GO	SSP1_AMSAL	Sex-specific storage protein 1 (SP-1) (Fragment)	0.00	-	exc	1 *	Secreted protein				56
Q9W7K2 UniProt NPD GO	NXS1_PSETE	Short neurotoxin 1/5 precursor (Alpha-neurotoxin 1/5)	0.00	-	mit	0	Secreted protein (By similarity)				79
Q9W7K0 UniProt NPD GO	NXS3_PSETE	Short neurotoxin 3 precursor (Alpha neurotoxin 3)	0.00	-	mit	0	Secreted protein (By similarity)				79
Q9W7J9 UniProt NPD GO	NXS4_PSETE	Short neurotoxin 4 precursor (Alpha neurotoxin 4)	0.00	-	mit	0	Secreted protein (By similarity)				79
Q9MYV9 UniProt NPD GO	TRPC5_BOVIN	Short transient receptor potential channel 5 (TrpC5) (Fragment)	0.00	-	exc	2 *	Membrane; multi-pass membrane protein (Probable)				109
P15367 UniProt NPD GO	SEC11_YEAST	Signal peptidase complex catalytic subunit SEC11 (EC 3.4.-.-)	0.00	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum [IDA] signal peptidase complex [IDA]			167
Q9VSC1 UniProt NPD GO	SRP09_DROME	Signal recognition particle 9 kDa protein homolog (SRP9)	0.00	-	cyt	0	Cytoplasm (By similarity)				77
O97374 UniProt NPD GO	SCP_LYMST	Small cardioactive peptides precursor [Contains: Small cardioactive peptide B (SCP B) (SCPb); Small ...	0.00	-	exc	0	Secreted protein				136
O82803 UniProt NPD GO	SRPP_HEVBR	Small rubber particle protein (SRPP) (22 kDa rubber particle protein) (22 kDa RPP) (Latex allergen H ...	0.00	-	cyt	0	Cytoplasm. Found in latex, the cytoplasm of laticifer cells. Tightly bound to small rubber particles ...				204
Q8MMH4 UniProt NPD GO	SVP2_PIMHY	Small venom protein 2 precursor	0.00	-	vac	0	Secreted protein				78
P48055 UniProt NPD GO	S6A12_RABIT	Sodium- and chloride-dependent betaine transporter (Na+/Cl-betaine/GABA transporter)	0.00	-	end	12 *	Membrane; multi-pass membrane protein				614
P28570 UniProt NPD GO	SC6A8_RAT	Sodium- and chloride-dependent creatine transporter 1 (CT1) (Creatine transporter 1) (CHOT1) (Solute ...	0.00	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [TAS]			635
O18875 UniProt NPD GO	SC6A8_BOVIN	Sodium- and chloride-dependent creatine transporter 1 (CT1) (Creatine transporter 1) (Solute carrier ...	0.00	-	end	12	Membrane; multi-pass membrane protein				635

You are viewing entries 98001 to 98050 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.