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
P11170 UniProt NPD GO	SC5A1_RABIT	Sodium/glucose cotransporter 1 (Na(+)/glucose cotransporter 1) (High affinity sodium-glucose cotrans ...	0.13	-	end	14 *	Membrane; multi-pass membrane protein				662
Q63008 UniProt NPD GO	SC5A5_RAT	Sodium/iodide cotransporter (Na(+)/I(-) cotransporter) (Sodium-iodide symporter) (Na(+)/I(-)-symport ...	0.13	-	end	13 *	Membrane; multi-pass membrane protein				618
P17326 UniProt NPD GO	AT1A_ARTSF	Sodium/potassium-transporting ATPase alpha chain (EC 3.6.3.9) (Sodium pump) (Na+/K+ ATPase)	0.13	-	end	8	Membrane; multi-pass membrane protein				996
P30715 UniProt NPD GO	AT1B1_BUFMA	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.13	-	mit	1 *	Membrane; single-pass type II membrane protein				303
P07340 UniProt NPD GO	AT1B1_RAT	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.13	-	mit	1 *	Membrane; single-pass type II membrane protein				304
P43002 UniProt NPD GO	AT1B2_BUFMA	Sodium/potassium-transporting ATPase subunit beta-2 (Sodium/potassium-dependent ATPase beta-2 subuni ...	0.13	-	cyt	1 *	Membrane; single-pass type II membrane protein				299
Q8AXS6 UniProt NPD GO	S35B1_XENTR	Solute carrier family 35 member B1	0.13	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				323
Q9VVD9 UniProt NPD GO	S35B3_DROME	Solute carrier family 35 member B3 homolog	0.13	-	end	10	Membrane; multi-pass membrane protein (Potential)				396
Q8K078 UniProt NPD GO	SO4A1_MOUSE	Solute carrier organic anion transporter family member 4A1 (Solute carrier family 21 member 12) (Sod ...	0.13	-	end	11	Membrane; multi-pass membrane protein				723
P19209 UniProt NPD GO	SMS_MYXGL	Somatostatin precursor [Contains: Somatostatin-34; Somatostatin-14] (Fragment)	0.13	-	nuc	0	Secreted protein				34
P35346 UniProt NPD GO	SSR5_HUMAN	Somatostatin receptor type 5 (SS5R)	0.13	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182455		364
O93566 UniProt NPD GO	SOMA_VERVA	Somatotropin precursor (Growth hormone)	0.13	-	exc	0	Secreted protein				203
O13235 UniProt NPD GO	SHH_DANAA	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
O13234 UniProt NPD GO	SHH_DANAE	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
O13238 UniProt NPD GO	SHH_DANAT	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
O13245 UniProt NPD GO	SHH_DANFR	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
P79709 UniProt NPD GO	SHH_DANKE	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
P79717 UniProt NPD GO	SHH_DANPU	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
O13241 UniProt NPD GO	SHH_DEVDE	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
O13247 UniProt NPD GO	SHH_DEVMA	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
O13250 UniProt NPD GO	SHH_DEVPA	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
P79915 UniProt NPD GO	SHH_TANAL	Sonic hedgehog protein (SHH) (Fragments)	0.13	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
Q62226 UniProt NPD GO	SHH_MOUSE	Sonic hedgehog protein precursor (SHH) (HHG-1) [Contains: Sonic hedgehog protein N-product; Sonic he ...	0.13	-	cyt	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space. Sonic hedgehog protein N-pr ...	cell surface [IDA] extracellular space [IDA] lipid raft [IDA]		1VHH	437
O62770 UniProt NPD GO	SP17_MACEU	Sperm surface protein Sp17 (Sperm autoantigenic protein 17)	0.13	+	nuc	0	Membrane; peripheral membrane protein (Potential)				153
O75602 UniProt NPD GO	SPAG6_HUMAN	Sperm-associated antigen 6 (PF16 protein homolog) (Sperm flagellar protein) (Repro-SA-1)	0.13	-	nuc	0	Cytoplasm. Associated with microtubules. Flagellum. Detected on the sperm flagellum	axoneme [TAS]	605730		509
Q20696 UniProt NPD GO	SMSR1_CAEEL	Sphingomyelin synthase-related 1	0.13	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			483
Q8BMS2 UniProt NPD GO	SPON2_MOUSE	Spondin-2 precursor (Mindin)	0.13	-	exc	0	Secreted protein; extracellular space; extracellular matrix				330
P17122 UniProt NPD GO	SPO16_YEAST	Sporulation-specific protein 16	0.13	-	cyt	0					198
Q9Y753 UniProt NPD GO	FDFT_YARLI	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.13	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				445
Q5EN22 UniProt NPD GO	ERG6_MAGGR	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.13	-	nuc	0					390
P25087 UniProt NPD GO	ERG6_YEAST	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.13	-	cyt	0		lipid particle [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			382
P53629 UniProt NPD GO	ARE2_YEAST	Sterol O-acyltransferase 2 (EC 2.3.1.26) (Sterol-ester synthase 2)	0.13	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			642
O82663 UniProt NPD GO	DHSA1_ARATH	Succinate dehydrogenase [ubiquinone] flavoprotein subunit 1, mitochondrial precursor (EC 1.3.5.1) (F ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane				634
Q9ZPX5 UniProt NPD GO	DHSA2_ARATH	Succinate dehydrogenase [ubiquinone] flavoprotein subunit 2, mitochondrial precursor (EC 1.3.5.1) (F ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			632
Q9BYC2 UniProt NPD GO	SCOT2_HUMAN	Succinyl-CoA:3-ketoacid-coenzyme A transferase 2, mitochondrial precursor (EC 2.8.3.5) (Testis-speci ...	0.13	-	mit	0	Mitochondrion	flagellum (sensu Eukaryota) [IDA] mitochondrion [IDA]			517
P49034 UniProt NPD GO	SUSY_ALNGL	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.13	-	nuc	0					803
P49039 UniProt NPD GO	SUS2_SOLTU	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase) (SS65)	0.13	-	mit	0					805
Q43009 UniProt NPD GO	SUS3_ORYSA	Sucrose synthase 3 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 3)	0.13	-	cyt	0					816
Q39232 UniProt NPD GO	SUC1_ARATH	Sucrose transport protein SUC1 (Sucrose permease 1) (Sucrose-proton symporter 1)	0.13	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				513
P23586 UniProt NPD GO	STP1_ARATH	Sugar transport protein 1 (Hexose transporter 1) (Glucose transporter)	0.13	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				522
P38359 UniProt NPD GO	SUL1_YEAST	Sulfate permease 1 (High-affinity sulfate transporter 1)	0.13	-	end	9	Membrane; multi-pass membrane protein	plasma membrane [IMP]			859
P21997 UniProt NPD GO	SSGP_VOLCA	Sulfated surface glycoprotein 185 precursor (SSG 185)	0.13	-	exc	0					485
O94284 UniProt NPD GO	HMT2_SCHPO	Sulfide:quinone oxidoreductase, mitochondrial precursor (EC 1.-.-.-) (Heavy metal tolerance protein ...	0.13	-	mit	0	Mitochondrion	mitochondrion [IDA]			459
Q29476 UniProt NPD GO	ST1A1_CANFA	Sulfotransferase 1A1 (EC 2.8.2.1) (Aryl sulfotransferase) (Phenol sulfotransferase) (Phenol-sulfatin ...	0.13	-	cyt	0	Cytoplasm (By similarity)				295
Q95JD5 UniProt NPD GO	ST1B1_CANFA	Sulfotransferase family cytosolic 1B member 1 (EC 2.8.2.-) (Sulfotransferase 1B1) (cSULT1B1)	0.13	-	cyt	0	Cytoplasm (By similarity)				296
Q9CY27 UniProt NPD GO	GPSN2_MOUSE	Synaptic glycoprotein SC2	0.13	-	cyt	4	Membrane; multi-pass membrane protein (Potential)				308
Q6CSA2 UniProt NPD GO	YKT6_KLULA	Synaptobrevin homolog YKT6	0.13	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
Q6C537 UniProt NPD GO	YKT6_YARLI	Synaptobrevin homolog YKT6	0.13	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
P01739 UniProt NPD GO	TVA2_MOUSE	T-cell receptor alpha chain V region 2B4 precursor	0.13	-	exc	0				1D9K	132
P06334 UniProt NPD GO	TCC3_MOUSE	T-cell receptor gamma chain C region DFL12	0.13	-	nuc	1				1YPZ	169

You are viewing entries 60451 to 60500 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.