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
Q8SQA6 UniProt NPD GO	CCL3_BOVIN	Small inducible cytokine A3 precursor (CCL3) (Macrophage inflammatory protein 1-alpha) (MIP-1-alpha) ...	0.03	-	exc	1 *	Secreted protein				93
P80162 UniProt NPD GO	SCYB6_HUMAN	Small inducible cytokine B6 precursor (CXCL6) (Granulocyte chemotactic protein 2) (GCP-2) (Chemokine ...	0.03	-	exc	0	Secreted protein		138965		114
Q9NY72 UniProt NPD GO	SCN3B_HUMAN	Sodium channel beta-3 subunit precursor	0.03	-	end	1 *	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	608214		215
Q8HXJ7 UniProt NPD GO	SCN3B_MACFA	Sodium channel beta-3 subunit precursor	0.03	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				215
Q8BHK2 UniProt NPD GO	SCN3B_MOUSE	Sodium channel beta-3 subunit precursor	0.03	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)				215
Q9JK00 UniProt NPD GO	SCN3B_RAT	Sodium channel beta-3 subunit precursor	0.03	-	mit	1	Membrane; single-pass type I membrane protein	integral to membrane [IDA]			215
P30531 UniProt NPD GO	SC6A1_HUMAN	Sodium- and chloride-dependent GABA transporter 1	0.03	-	end	12	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. Localized at the ...	integral to membrane [TAS] membrane fraction [TAS]	137165		599
P31648 UniProt NPD GO	SC6A1_MOUSE	Sodium- and chloride-dependent GABA transporter 1	0.03	-	end	12	Cell membrane; multi-pass membrane protein (By similarity). Membrane; multi-pass membrane protein (B ...	axon [IDA]			599
P23978 UniProt NPD GO	SC6A1_RAT	Sodium- and chloride-dependent GABA transporter 1	0.03	-	end	12	Cell membrane; multi-pass membrane protein (By similarity). Localized at the presynaptic terminals o ...				599
Q9NSD5 UniProt NPD GO	S6A13_HUMAN	Sodium- and chloride-dependent GABA transporter 2	0.03	-	end	12 *	Membrane; multi-pass membrane protein				569
P31646 UniProt NPD GO	S6A13_RAT	Sodium- and chloride-dependent GABA transporter 2	0.03	-	end	12 *	Membrane; multi-pass membrane protein				602
P31649 UniProt NPD GO	S6A13_MOUSE	Sodium- and chloride-dependent GABA transporter 3 (GAT3)	0.03	-	end	12 *	Membrane; multi-pass membrane protein				602
P28571 UniProt NPD GO	SC6A9_MOUSE	Sodium- and chloride-dependent glycine transporter 1 (GlyT1) (GlyT-1) (Solute carrier family 6 membe ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein				633
P28572 UniProt NPD GO	SC6A9_RAT	Sodium- and chloride-dependent glycine transporter 1 (GlyT1) (GlyT-1) (Solute carrier family 6 membe ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein				633
Q761V0 UniProt NPD GO	SC6A5_MOUSE	Sodium- and chloride-dependent glycine transporter 2 (GlyT2) (GlyT-2) (Solute carrier family 6 membe ...	0.03	-	end	12	Membrane; multi-pass membrane protein (By similarity)				799
P58295 UniProt NPD GO	SC6A5_RAT	Sodium- and chloride-dependent glycine transporter 2 (GlyT2) (GlyT-2) (Solute carrier family 6 membe ...	0.03	-	end	12	Membrane; multi-pass membrane protein				799
Q9JMA9 UniProt NPD GO	S6A14_MOUSE	Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) (Amino acid transporte ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein				638
Q9MZ34 UniProt NPD GO	SC6A6_BOVIN	Sodium- and chloride-dependent taurine transporter	0.03	-	end	12 *	Membrane; multi-pass membrane protein				620
Q9NP91 UniProt NPD GO	S6A20_HUMAN	Sodium- and chloride-dependent transporter XTRP3 (Solute carrier family 6 member 20) (Neurotransmitt ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [TAS]	605616		592
Q21339 UniProt NPD GO	NAD3_CAEEL	Sodium-dependent high-affinity dicarboxylate transporter 3 (Na(+)/dicarboxylate cotransporter 3) (Na ...	0.03	-	end	12	Membrane; multi-pass membrane protein (Potential)				566
Q5R6J1 UniProt NPD GO	S6A19_PONPY	Sodium-dependent neutral amino acid transporter B(0) (System B(0) neutral amino acid transporter) (B ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				634
Q60489 UniProt NPD GO	AT1B3_CAVPO	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.03	-	mit	1 *	Membrane; single-pass type II membrane protein				279
Q925Q3 UniProt NPD GO	NCKX6_MOUSE	Sodium/potassium/calcium exchanger 6 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 6) (Solute carrie ...	0.03	-	end	13 *	Membrane; multi-pass membrane protein. Isoform 2 localizes to the plasma membrane. Isoform 1 may loc ...				585
Q8VCF1 UniProt NPD GO	CANT1_MOUSE	Soluble calcium-activated nucleotidase 1 (EC 3.6.1.6) (SCAN-1) (Apyrase homolog)	0.03	-	mit	0	Intracytoplasmic membrane; single-pass type II membrane protein (By similarity). Secreted protein (B ...				403
Q40739 UniProt NPD GO	SSY1_ORYSA	Soluble starch synthase 1, chloroplast precursor (EC 2.4.1.21) (Starch synthase I) (SSS 1)	0.03	-	mit	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Soluble	amyloplast [IDA]			626
Q13183 UniProt NPD GO	S13A2_HUMAN	Solute carrier family 13 member 2 (Renal sodium/dicarboxylate cotransporter) (Na(+)/dicarboxylate co ...	0.03	-	end	11 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] membrane fraction [TAS]	604148		592
Q8WWT9 UniProt NPD GO	S13A3_HUMAN	Solute carrier family 13 member 3 (Sodium-dependent high-affinity dicarboxylate transporter 2) (Na(+ ...	0.03	-	end	11 *	Membrane; multi-pass membrane protein		606411		602
P46896 UniProt NPD GO	GTR1_CHICK	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1) (GT1) ...	0.03	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...				490
P13355 UniProt NPD GO	GTR1_RABIT	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.03	-	end	10 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...				492
P11167 UniProt NPD GO	GTR1_RAT	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.03	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...	integral to membrane [TAS]			492
P20303 UniProt NPD GO	GTR1_PIG	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.03	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...				451
P79365 UniProt NPD GO	GTR1_SHEEP	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.03	-	end	8 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...				390
P17809 UniProt NPD GO	GTR1_MOUSE	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.03	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...	intracellular [IDA] plasma membrane [IDA]			492
P11166 UniProt NPD GO	GTR1_HUMAN	Solute carrier family 2, facilitated glucose transporter member 1 (Glucose transporter type 1, eryth ...	0.03	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity). Localizes primarily at the cell surface ...	membrane [TAS] membrane fraction [TAS]	138140	1SUK	492
P58351 UniProt NPD GO	GTR2_BOVIN	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter type 2, liver ...	0.03	-	end	3 *	Membrane; multi-pass membrane protein				142
P32037 UniProt NPD GO	GTR3_MOUSE	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.03	-	end	10 *	Membrane; multi-pass membrane protein				493
Q9WV38 UniProt NPD GO	GTR5_MOUSE	Solute carrier family 2, facilitated glucose transporter member 5 (Glucose transporter type 5, small ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein				501
Q9JIF3 UniProt NPD GO	GTR8_MOUSE	Solute carrier family 2, facilitated glucose transporter member 8 (Glucose transporter type 8) (Gluc ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein. Principally intracellular. May move between intracellular ves ...	integral to plasma membrane [IDA]			477
Q9PRR0 UniProt NPD GO	SMS_LAMFL	Somatostatin precursor [Contains: Somatostatin-35; Somatostatin-14] (Fragment)	0.03	-	cyt	0	Secreted protein				35
P08899 UniProt NPD GO	SOMA_ANGJA	Somatotropin-1 precursor (Somatotropin I) (Growth hormone I)	0.03	-	mit	0	Secreted protein				209
Q9XXL3 UniProt NPD GO	SSP31_CAEEL	Sperm-specific protein 31	0.03	-	cyt	0					107
Q9XY92 UniProt NPD GO	SPEE_DICDI	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.03	-	mit	0					284
P09351 UniProt NPD GO	SR1B_PHYPO	Spherulin-1B precursor	0.03	-	exc	0	Cell wall				248
P09352 UniProt NPD GO	SR2A_PHYPO	Spherulin-2A	0.03	-	cyt	0					315
O95136 UniProt NPD GO	EDG5_HUMAN	Sphingosine 1-phosphate receptor Edg-5 (S1P receptor Edg-5) (Endothelial differentiation G-protein c ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein		605111	1ZTI	353
P46802 UniProt NPD GO	SPD1_ARABI	Spidroin 1 (Dragline silk fibroin 1) (Fragment)	0.03	-	nuc	0	Secreted protein; extracellular space				79
Q6FMI2 UniProt NPD GO	DIB1_CANGA	Spliceosomal protein DIB1	0.03	-	cyt	0	Nucleus (By similarity)				142
P15520 UniProt NPD GO	SPG2_DICDI	Spore germination protein 2 precursor (SPG2)	0.03	-	mit	1 *	Secreted protein (Probable)				127
P35173 UniProt NPD GO	CYT1_MOUSE	Stefin 1	0.03	-	cyt	0	Cytoplasm (By similarity)				103
P35478 UniProt NPD GO	CYTX_BOVIN	Stefin C	0.03	-	cyt	0	Cytoplasm				101

You are viewing entries 81701 to 81750 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.