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
P84830 UniProt NPD GO	SKSP5_ASCTR	Skin secreted peptide 5	0.02	-		0	Secreted protein	extracellular region [IDA]			15
Q8I021 UniProt NPD GO	CCL17_FELCA	Small inducible cytokine A17 precursor (CCL17) (Thymus and activation-regulated chemokine) (CC chemo ...	0.02	-	exc	0	Secreted protein				99
Q12330 UniProt NPD GO	RUXE_YEAST	Small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.02	-	cyt	0	Cytoplasm. Nucleus	snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			94
Q24297 UniProt NPD GO	RUXF_DROME	Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF) (Membrane-associated protein ...	0.02	-	cyt	0	Nucleus	small nuclear ribonucleoprotein complex [NAS]			88
Q3ZBL0 UniProt NPD GO	RUXG_BOVIN	Small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.02	-	mit	0	Nucleus (By similarity)				76
P62308 UniProt NPD GO	RUXG_HUMAN	Small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.02	-	mit	0	Nucleus	small nuclear ribonucleoprotein complex [NAS] spliceosome complex [TAS]	603542		76
P62309 UniProt NPD GO	RUXG_MOUSE	Small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.02	-	mit	0	Nucleus (By similarity)	small nuclear ribonucleoprotein complex [ISS] spliceosome complex [ISS]			76
P40204 UniProt NPD GO	RUXG_YEAST	Small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.02	-	nuc	0	Nucleus	snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			77
P15229 UniProt NPD GO	SCX1_BUTSI	Small toxin (Peptide I) (Chlorotoxin-like peptide Bs 8) (Bs8)	0.02	-	nuc	0	Secreted protein				35
Q84TI7 UniProt NPD GO	HKT1_ARATH	Sodium transporter HKT1 (AtHKT1)	0.02	-	end	10 *	Cell membrane; multi-pass membrane protein				506
P48066 UniProt NPD GO	S6A11_HUMAN	Sodium- and chloride-dependent GABA transporter 3	0.02	-	end	10	Membrane; multi-pass membrane protein	integral to membrane [TAS]	607952		632
Q9Y345 UniProt NPD GO	SC6A5_HUMAN	Sodium- and chloride-dependent glycine transporter 2 (GlyT2) (GlyT-2) (Solute carrier family 6 membe ...	0.02	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [TAS]	604159		797
Q00589 UniProt NPD GO	SC6A6_CANFA	Sodium- and chloride-dependent taurine transporter	0.02	-	end	12 *	Membrane; multi-pass membrane protein				620
P31641 UniProt NPD GO	SC6A6_HUMAN	Sodium- and chloride-dependent taurine transporter	0.02	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	186854		620
O88576 UniProt NPD GO	S6A18_MOUSE	Sodium- and chloride-dependent transporter XTRP2 (Solute carrier family 6 member 18)	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]			615
Q7YT61 UniProt NPD GO	SCX5C_CENLL	Sodium-channel modifier toxin Cll5c precursor	0.02	-	exc	0	Secreted protein (By similarity)				87
Q7Z1K6 UniProt NPD GO	SCX5X_CENLL	Sodium-channel modifier toxin Cll5c* precursor	0.02	-	exc	1 *	Secreted protein (By similarity)				85
O70247 UniProt NPD GO	SC5A6_RAT	Sodium-dependent multivitamin transporter (Na(+)-dependent multivitamin transporter)	0.02	-	end	13 *	Membrane; multi-pass membrane protein				634
Q695T7 UniProt NPD GO	S6A19_HUMAN	Sodium-dependent neutral amino acid transporter B(0) (System B(0) neutral amino acid transporter) (B ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Probable)		608893		634
Q80SU6 UniProt NPD GO	NPT2C_MOUSE	Sodium-dependent phosphate transport protein 2C (Sodium/phosphate cotransporter 2C) (Na(+)/Pi cotran ...	0.02	-	end	11	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] brush border [IDA]			601
Q8K4R8 UniProt NPD GO	NPT2C_RAT	Sodium-dependent phosphate transport protein 2C (Sodium/phosphate cotransporter 2C) (Na(+)/Pi cotran ...	0.02	-	end	11	Membrane; multi-pass membrane protein	apical plasma membrane [IDA]			601
P13638 UniProt NPD GO	AT1B2_RAT	Sodium/potassium-transporting ATPase subunit beta-2 (Sodium/potassium-dependent ATPase beta-2 subuni ...	0.02	-	cyt	1 *	Membrane; single-pass type II membrane protein	apical plasma membrane [IDA]			290
Q3T0C6 UniProt NPD GO	AT1B3_BOVIN	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.02	-	mit	1 *	Membrane; single-pass type II membrane protein				279
Q8NFF2 UniProt NPD GO	NCKX4_HUMAN	Sodium/potassium/calcium exchanger 4 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 4) (Solute carrie ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein		609840		605
Q6AXS0 UniProt NPD GO	NCKX6_RAT	Sodium/potassium/calcium exchanger 6 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 6) (Solute carrie ...	0.02	-	end	12	Cell membrane; multi-pass membrane protein				585
Q8K4Y7 UniProt NPD GO	CANT1_RAT	Soluble calcium-activated nucleotidase 1 (EC 3.6.1.6) (SCAN-1) (Apyrase homolog)	0.02	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	endoplasmic reticulum membrane [IDA]			403
Q9VEU6 UniProt NPD GO	GCYDA_DROME	Soluble guanylate cyclase 89Da (EC 4.6.1.2)	0.02	-	cyt	0	Cytoplasm (By similarity)	guanylate cyclase complex, soluble [IC]			667
P21216 UniProt NPD GO	IPYR_ARATH	Soluble inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm (By similarity)				218
Q9JHI4 UniProt NPD GO	S13A1_MOUSE	Solute carrier family 13 member 1 (Renal sodium/sulfate cotransporter) (Na(+)/sulfate cotransporter) ...	0.02	-	end	9 *	Membrane; multi-pass membrane protein				594
P58352 UniProt NPD GO	GTR3_BOVIN	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein				494
Q07647 UniProt NPD GO	GTR3_RAT	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein				493
P47843 UniProt NPD GO	GTR3_SHEEP	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein				494
Q9XST2 UniProt NPD GO	GTR4_CANFA	Solute carrier family 2, facilitated glucose transporter member 4 (Glucose transporter type 4, insul ...	0.02	-	end	5 *	Intracytoplasmic membrane; perinuclear region; multi-pass membrane protein (By similarity). Localize ...				162
P46408 UniProt NPD GO	GTR5_RABIT	Solute carrier family 2, facilitated glucose transporter member 5 (Glucose transporter type 5, small ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein				486
P43427 UniProt NPD GO	GTR5_RAT	Solute carrier family 2, facilitated glucose transporter member 5 (Glucose transporter type 5, small ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein	membrane [IDA]			502
Q9JJZ1 UniProt NPD GO	GTR8_RAT	Solute carrier family 2, facilitated glucose transporter member 8 (Glucose transporter type 8) (Gluc ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein. Principally intracellular. May move between intracellular ves ...				478
Q80UJ1 UniProt NPD GO	OAT6_MOUSE	Solute carrier family 22 member 20 (Organic anion transporter 6)	0.02	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				556
Q9UHI7 UniProt NPD GO	S23A1_HUMAN	Solute carrier family 23 member 1 (Sodium-dependent vitamin C transporter 1) (hSVCT1) (Na(+)/L-ascor ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603790		598
Q9I9R3 UniProt NPD GO	S40A1_BRARE	Solute carrier family 40 member 1 (Ferroportin-1)	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				562
P46720 UniProt NPD GO	SO1A1_RAT	Solute carrier organic anion transporter family member 1A1 (Solute carrier family 21 member 1) (Sodi ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			670
P69134 UniProt NPD GO	SMS1_ANGAN	Somatostatin-1 (Somatostatin I)	0.02	-		0	Secreted protein				14
P69132 UniProt NPD GO	SMS1_MYOSC	Somatostatin-1 (Somatostatin I)	0.02	-		0	Secreted protein				14
P69133 UniProt NPD GO	SMS1_ONCKI	Somatostatin-1 (Somatostatin I)	0.02	-		0	Secreted protein				14
P61298 UniProt NPD GO	SMS_ALLMI	Somatostatin-14	0.02	-		0	Secreted protein				14
P61299 UniProt NPD GO	SMS_TRASC	Somatostatin-14	0.02	-		0	Secreted protein				14
P79839 UniProt NPD GO	SHH_PSEPR	Sonic hedgehog protein (SHH) (Fragment)	0.02	-	nuc	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				58
P19852 UniProt NPD GO	MOSH_CLYJA	Sperm-activating peptide SAP-b ([His6]-mosact)	0.02	-		0					9
Q9Y8H7 UniProt NPD GO	SPEE_NEUCR	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.02	-	cyt	0					291
Q9ZUB3 UniProt NPD GO	SPD1_ARATH	Spermidine synthase 1 (EC 2.5.1.16) (Putrescine aminopropyltransferase 1) (SPDSY 1)	0.02	-	cyt	0				1XJ5	334
Q96LT4 UniProt NPD GO	SAMD8_HUMAN	Sphingomyelin synthase-related 1 (Sterile alpha motif domain-containing 8)	0.02	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			415

You are viewing entries 85751 to 85800 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.