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
P61009 UniProt NPD GO	SPCS3_HUMAN	Signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 23 kDa subunit) (SPase ...	0.01	-	end	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				180
P28687 UniProt NPD GO	SPCS3_CHICK	Signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 23 kDa subunit) (SPase ...	0.01	-	vac	1 *	Microsome; microsomal membrane; single-pass type II membrane protein				180
Q6Z2T3 UniProt NPD GO	LSI1_ORYSA	Silicon transporter LSI1 (Low silicon protein 1)	0.01	-	end	6	Cell membrane; multi-pass membrane protein				298
P84828 UniProt NPD GO	SKSP3_ASCTR	Skin secreted peptide 3	0.01	-		0	Secreted protein	extracellular region [IDA]			12
P84829 UniProt NPD GO	SKSP4_ASCTR	Skin secreted peptide 4	0.01	-		0	Secreted protein	extracellular region [IDA]			8
O88430 UniProt NPD GO	CCL22_MOUSE	Small inducible cytokine A22 precursor (CCL22) (CC chemokine ABCD-1) (Activated B and dendritic cell ...	0.01	-	exc	0	Secreted protein				92
O00626 UniProt NPD GO	CCL22_HUMAN	Small inducible cytokine A22 precursor (CCL22) (Macrophage-derived chemokine) (MDC(1-69)) (Stimulate ...	0.01	-	exc	1 *	Secreted protein	extracellular space [TAS]	602957		93
Q90826 UniProt NPD GO	CCL4_CHICK	Small inducible cytokine A4 homolog precursor (Macrophage inflammatory protein 1-beta homolog)	0.01	-	exc	0	Secreted protein				90
O14625 UniProt NPD GO	SCYBB_HUMAN	Small inducible cytokine B11 precursor (CXCL11) (Interferon-inducible T-cell alpha chemoattractant) ...	0.01	-	end	1 *	Secreted protein		604852	1RJT	94
P80221 UniProt NPD GO	SCYB6_BOVIN	Small inducible cytokine B6 precursor (CXCL6) (Granulocyte chemotactic protein 2) (GCP-2)	0.01	-	exc	0	Secreted protein				112
P62306 UniProt NPD GO	RUXF_HUMAN	Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus		603541		86
P62307 UniProt NPD GO	RUXF_MOUSE	Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus (By similarity)				86
P62321 UniProt NPD GO	RUXF_XENLA	Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus (By similarity)				86
P54999 UniProt NPD GO	RUXF_YEAST	Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus	snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]		1N9S	86
Q8MMH5 UniProt NPD GO	SVP1_PIMHY	Small venom protein 1 precursor	0.01	-	exc	1 *	Secreted protein				61
P31647 UniProt NPD GO	S6A11_RAT	Sodium- and chloride-dependent GABA transporter 3	0.01	-	end	10	Membrane; multi-pass membrane protein				627
P31650 UniProt NPD GO	S6A11_MOUSE	Sodium- and chloride-dependent GABA transporter 4 (GAT4)	0.01	-	end	10	Membrane; multi-pass membrane protein				627
Q9UN76 UniProt NPD GO	S6A14_HUMAN	Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) (Amino acid transporte ...	0.01	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	300444		642
Q62687 UniProt NPD GO	S6A18_RAT	Sodium- and chloride-dependent transporter XTRP2 (Solute carrier family 6 member 18) (Renal osmotic ...	0.01	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				615
O88575 UniProt NPD GO	S6A20_MOUSE	Sodium- and chloride-dependent transporter XTRP3 (Solute carrier family 6 member 20)	0.01	-	end	12	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			635
P59865 UniProt NPD GO	SCX7_CENLL	Sodium-channel modifier neurotoxin Cll7 precursor	0.01	-	vac	1 *	Secreted protein				85
Q7Z1K9 UniProt NPD GO	SCX3_CENLL	Sodium-channel modifier toxin Cll3 precursor	0.01	-	mit	1 *	Secreted protein (By similarity)				87
Q9Y289 UniProt NPD GO	SC5A6_HUMAN	Sodium-dependent multivitamin transporter (Na(+)-dependent multivitamin transporter)	0.01	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604024		635
Q5U4D8 UniProt NPD GO	SC5A6_MOUSE	Sodium-dependent multivitamin transporter (Na(+)-dependent multivitamin transporter)	0.01	-	end	13 *	Membrane; multi-pass membrane protein				634
Q6PGE7 UniProt NPD GO	SC6A7_MOUSE	Sodium-dependent proline transporter (Solute carrier family 6 member 7)	0.01	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)				637
P28573 UniProt NPD GO	SC6A7_RAT	Sodium-dependent proline transporter (Solute carrier family 6 member 7)	0.01	-	end	12 *	Membrane; multi-pass membrane protein				637
O35899 UniProt NPD GO	SC6A4_CAVPO	Sodium-dependent serotonin transporter (5HT transporter) (5HTT)	0.01	-	end	12	Membrane; multi-pass membrane protein				630
P51905 UniProt NPD GO	SC6A4_DROME	Sodium-dependent serotonin transporter (5HT transporter) (5HTT) (Cocaine-sensitive serotonin transpo ...	0.01	-	end	12	Membrane; multi-pass membrane protein				622
P14231 UniProt NPD GO	AT1B2_MOUSE	Sodium/potassium-transporting ATPase subunit beta-2 (Sodium/potassium-dependent ATPase beta-2 subuni ...	0.01	-	cyt	1 *	Membrane; single-pass type II membrane protein	cytoplasm [IDA]			290
P54709 UniProt NPD GO	AT1B3_HUMAN	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.01	-	mit	1 *	Membrane; single-pass type II membrane protein	sodium:potassium-exchanging ATPase complex [TAS]	601867		279
Q8CGQ8 UniProt NPD GO	NCKX4_MOUSE	Sodium/potassium/calcium exchanger 4 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 4)	0.01	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			605
O22537 UniProt NPD GO	IPYR_ORYSA	Soluble inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.01	-	cyt	0	Cytoplasm				214
P93568 UniProt NPD GO	SSY1_SOLTU	Soluble starch synthase 1, chloroplast precursor (EC 2.4.1.21) (SS I) (Soluble starch synthase I)	0.01	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Soluble				641
Q07782 UniProt NPD GO	S13A1_RAT	Solute carrier family 13 member 1 (Renal sodium/sulfate cotransporter) (Na(+)/sulfate cotransporter) ...	0.01	-	end	9 *	Membrane; multi-pass membrane protein	brush border [IPI]			595
O62786 UniProt NPD GO	GTR2_PIG	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter type 2, liver ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein				120
P28568 UniProt NPD GO	GTR3_CHICK	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3) (CEF- ...	0.01	-	end	10 *	Membrane; multi-pass membrane protein				496
Q9XSC2 UniProt NPD GO	GTR3_RABIT	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.01	-	end	8 *	Membrane; multi-pass membrane protein				400
P22732 UniProt NPD GO	GTR5_HUMAN	Solute carrier family 2, facilitated glucose transporter member 5 (Glucose transporter type 5, small ...	0.01	-	end	12 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	138230		501
P58354 UniProt NPD GO	GTR8_BOVIN	Solute carrier family 2, facilitated glucose transporter member 8 (Glucose transporter type 8) (Gluc ...	0.01	-	end	12 *	Membrane; multi-pass membrane protein. Principally intracellular. May move between intracellular ves ...				478
P09876 UniProt NPD GO	SMS2_MYOSC	Somatostatin-2 precursor (Somatostatin II) [Contains: [Tyr21,Gly24]-somatostatin-28; [Tyr7,Gly10]-so ...	0.01	-	mit	0	Secreted protein				74
Q58D31 UniProt NPD GO	DHSO_BOVIN	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase)	0.01	-	cyt	0					355
P27867 UniProt NPD GO	DHSO_RAT	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase)	0.01	-	mit	0					399
P07846 UniProt NPD GO	DHSO_SHEEP	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase)	0.01	-	cyt	0				1SDG	354
Q29318 UniProt NPD GO	DHSO_PIG	Sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase) (Fragment)	0.01	-	cyt	0					96
P87218 UniProt NPD GO	SOU2_CANAL	Sorbitol utilization protein SOU2 (EC 1.1.-.-)	0.01	-	cyt	0					280
P24047 UniProt NPD GO	SAP_STOVA	Sperm-activating peptide (SAP)	0.01	-		0					9
Q23246 UniProt NPD GO	SSPZC_CAEEL	Sperm-specific protein ZC168.6	0.01	-	nuc	0				1M1S	107
Q9SMB1 UniProt NPD GO	SPD1_ORYSA	Spermidine synthase 1 (EC 2.5.1.16) (Putrescine aminopropyltransferase 1) (SPDSY 1)	0.01	-	cyt	0					323
Q12455 UniProt NPD GO	SPSY_YEAST	Spermine synthase (EC 2.5.1.22) (Spermidine aminopropyltransferase) (SPMSY)	0.01	-	cyt	0		cytoplasm [IDA]			300
P09350 UniProt NPD GO	SR1A_PHYPO	Spherulin-1A precursor	0.01	-	exc	0	Cell wall				246

You are viewing entries 91501 to 91550 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.)

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