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
P48029 UniProt NPD GO	SC6A8_HUMAN	Sodium- and chloride-dependent creatine transporter 1 (CT1) (Creatine transporter 1) (Solute carrier ...	0.00	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [TAS]	300352		635
Q8VBW1 UniProt NPD GO	SC6A8_MOUSE	Sodium- and chloride-dependent creatine transporter 1 (CT1) (Creatine transporter 1) (Solute carrier ...	0.00	-	end	12	Membrane; multi-pass membrane protein (By similarity)				640
P31661 UniProt NPD GO	SC6A8_RABIT	Sodium- and chloride-dependent creatine transporter 1 (CT1) (Creatine transporter 1) (Solute carrier ...	0.00	-	end	12	Membrane; multi-pass membrane protein				635
O35316 UniProt NPD GO	SC6A6_MOUSE	Sodium- and chloride-dependent taurine and beta-alanine transporter	0.00	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			621
P31643 UniProt NPD GO	SC6A6_RAT	Sodium- and chloride-dependent taurine transporter	0.00	-	end	12 *	Membrane; multi-pass membrane protein				621
Q7Z1K5 UniProt NPD GO	SCX6_CENLL	Sodium-channel modifier toxin Cll6 precursor	0.00	-	vac	1 *	Secreted protein (By similarity)				85
Q7Z1K4 UniProt NPD GO	SCX8_CENLL	Sodium-channel modifier toxin Cll8 precursor (Fragment)	0.00	-	nuc	0	Secreted protein (By similarity)				72
Q01959 UniProt NPD GO	SC6A3_HUMAN	Sodium-dependent dopamine transporter (DA transporter) (DAT)	0.00	-	end	12	Membrane; multi-pass membrane protein	cytoplasm [TAS] integral to membrane [TAS] plasma membrane [IDA]	126455		620
Q9GJT6 UniProt NPD GO	SC6A3_MACFA	Sodium-dependent dopamine transporter (DA transporter) (DAT)	0.00	-	end	12	Membrane; multi-pass membrane protein (By similarity)				620
Q61327 UniProt NPD GO	SC6A3_MOUSE	Sodium-dependent dopamine transporter (DA transporter) (DAT)	0.00	-	end	12	Membrane; multi-pass membrane protein (By similarity)				619
P23977 UniProt NPD GO	SC6A3_RAT	Sodium-dependent dopamine transporter (DA transporter) (DAT)	0.00	-	end	12	Membrane; multi-pass membrane protein				619
Q9D687 UniProt NPD GO	S6A19_MOUSE	Sodium-dependent neutral amino acid transporter B(0) (System B(0) neutral amino acid transporter) (B ...	0.00	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				634
Q99884 UniProt NPD GO	SC6A7_HUMAN	Sodium-dependent proline transporter (Solute carrier family 6 member 7)	0.00	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	606205		636
P14415 UniProt NPD GO	AT1B2_HUMAN	Sodium/potassium-transporting ATPase subunit beta-2 (Sodium/potassium-dependent ATPase beta-2 subuni ...	0.00	-	cyt	1 *	Membrane; single-pass type II membrane protein		182331		290
Q8WVQ1 UniProt NPD GO	CANT1_HUMAN	Soluble calcium-activated nucleotidase 1 (EC 3.6.1.6) (SCAN-1) (Apyrase homolog) (Putative NF-kappa- ...	0.00	-	mit	0	Intracytoplasmic membrane; single-pass type II membrane protein. Processed form: Secreted protein			1S1D	401
Q863Y9 UniProt NPD GO	GTR5_HORSE	Solute carrier family 2, facilitated glucose transporter member 5 (Glucose transporter type 5, small ...	0.00	-	end	12 *	Membrane; multi-pass membrane protein				501
P58353 UniProt NPD GO	GTR5_BOVIN	Solute carrier family 2, facilitated glucose transporter member 5 (Glucose transporter type 5, small ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein				204
Q9VDD7 UniProt NPD GO	S35B1_DROME	Solute carrier family 35 member B1 homolog	0.00	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [NAS]			338
Q9NQQ7 UniProt NPD GO	S35C2_HUMAN	Solute carrier family 35 member C2 (Ovarian cancer overexpressed gene 1 protein)	0.00	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				365
Q8VCX2 UniProt NPD GO	S35C2_MOUSE	Solute carrier family 35 member C2 (Ovarian cancer overexpressed gene 1 protein)	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				364
Q02912 UniProt NPD GO	DHSO_BOMMO	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase)	0.00	-	end	0					348
Q00796 UniProt NPD GO	DHSO_HUMAN	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase)	0.00	-	cyt	0			182500	1PL8	356
Q4R639 UniProt NPD GO	DHSO_MACFA	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase)	0.00	-	cyt	0					356
Q64442 UniProt NPD GO	DHSO_MOUSE	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase) (Fragment)	0.00	-	mit	0					375
P35497 UniProt NPD GO	DHSO1_YEAST	Sorbitol dehydrogenase 1 (EC 1.1.1.14) (L-iditol 2-dehydrogenase 1)	0.00	-	cyt	0					357
Q07786 UniProt NPD GO	DHSO2_YEAST	Sorbitol dehydrogenase 2 (EC 1.1.1.14) (L-iditol 2-dehydrogenase 2)	0.00	-	cyt	0					357
Q7M3P1 UniProt NPD GO	TXV1_PHONI	Spasmogenic toxin PnV1 (Fragment)	0.00	-		0	Secreted protein				8
P83569 UniProt NPD GO	SAPP_SEPOF	Sperm attracting peptide SepSAP	0.00	-		0	Secreted protein				6
Q21289 UniProt NPD GO	SSP10_CAEEL	Sperm-specific protein 10	0.00	-	cyt	0					109
P91499 UniProt NPD GO	SSP16_CAEEL	Sperm-specific protein 16	0.00	-	cyt	0					109
O01829 UniProt NPD GO	SSP19_CAEEL	Sperm-specific protein 19	0.00	-	cyt	0				1ROW	109
O45433 UniProt NPD GO	SSP32_CAEEL	Sperm-specific protein 32	0.00	-	cyt	0					107
Q23058 UniProt NPD GO	SSP9_CAEEL	Sperm-specific protein 9/11	0.00	-	cyt	0					109
O48660 UniProt NPD GO	SPDE_NICSY	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (Aminopropyltransferase)	0.00	-	cyt	0					314
O82147 UniProt NPD GO	SPDE_COFAR	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.00	-	cyt	0					316
Q9ZS45 UniProt NPD GO	SPDE_LYCES	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.00	-	cyt	0					342
Q09741 UniProt NPD GO	SPEE_SCHPO	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.00	-	cyt	0					298
Q12074 UniProt NPD GO	SPEE_YEAST	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			293
Q96556 UniProt NPD GO	SPD1_DATST	Spermidine synthase 1 (EC 2.5.1.16) (Putrescine aminopropyltransferase 1) (SPDSY 1)	0.00	-	cyt	0					308
O48658 UniProt NPD GO	SPD1_HYONI	Spermidine synthase 1 (EC 2.5.1.16) (Putrescine aminopropyltransferase 1) (SPDSY 1)	0.00	-	cyt	0					315
O48661 UniProt NPD GO	SPD2_ARATH	Spermidine synthase 2 (EC 2.5.1.16) (Putrescine aminopropyltransferase 2) (SPDSY 2)	0.00	-	cyt	0					340
Q96557 UniProt NPD GO	SPD2_DATST	Spermidine synthase 2 (EC 2.5.1.16) (Putrescine aminopropyltransferase 2) (SPDSY 2)	0.00	-	cyt	0					317
O48659 UniProt NPD GO	SPD2_HYONI	Spermidine synthase 2 (EC 2.5.1.16) (Putrescine aminopropyltransferase 2) (SPDSY 2)	0.00	-	cyt	0					308
P09353 UniProt NPD GO	SR3A_PHYPO	Spherulin 3A (S3A)	0.00	-	cyt	0	Cytoplasm			1HDF	103
O70572 UniProt NPD GO	NSMA_MOUSE	Sphingomyelin phosphodiesterase 2 (EC 3.1.4.12) (Neutral sphingomyelinase) (nSMase) (N-SMase) (Lyso- ...	0.00	-	end	2	Membrane; multi-pass membrane protein				419
Q8I914 UniProt NPD GO	SMA1_LOXLA	Sphingomyelinase D 1 precursor (Sphingomyelinase I) (EC 3.1.4.41) (SMase I)	0.00	-	vac	0	Secreted protein			2F9R	311
P69502 UniProt NPD GO	SMAL_LOXGA	Sphingomyelinase loxnecrogin (EC 3.1.4.41) (SMase) (Dermonecrotic protein) (Fragments)	0.00	-	cyt	0	Secreted protein				71
P47752 UniProt NPD GO	EDG5_RAT	Sphingosine 1-phosphate receptor Edg-5 (S1P receptor Edg-5) (G-protein coupled receptor H218) (AGR16 ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
P52592 UniProt NPD GO	EDG5_MOUSE	Sphingosine 1-phosphate receptor Edg-5 (S1P receptor Edg-5) (Lysophospholipid receptor B2) (Endothel ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
Q9QXN2 UniProt NPD GO	RSP1_RAT	Spleen protein 1 precursor (Protein RSP-1)	0.00	-	exc	1 *	Secreted protein				99

You are viewing entries 98051 to 98100 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.