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
Q27967 UniProt NPD GO	SPP24_BOVIN	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.33	-	nuc	0	Secreted protein				203
Q70TH4 UniProt NPD GO	SPP24_SHEEP	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.33	-	nuc	0	Secreted protein (By similarity)				203
P09683 UniProt NPD GO	SECR_HUMAN	Secretin precursor	0.33	-	exc	0	Secreted protein		182099		121
Q9ESM7 UniProt NPD GO	SEL1L_MESAU	Sel-1 homolog precursor (Suppressor of lin-12-like protein) (Sel-1L)	0.33	-	end	0	Membrane; single-pass type I membrane protein (Potential)				794
P16531 UniProt NPD GO	SVP2_CAVPO	Seminal vesicle protein SVP-2 precursor (Fragment)	0.33	-	nuc	0					132
P04812 UniProt NPD GO	SVS5_RAT	Seminal vesicle secretory protein 5 precursor (Seminal vesicle secretory protein V) (SVS V) (SVS pro ...	0.33	-	exc	0	Secreted protein; extracellular space				123
Q93YV6 UniProt NPD GO	2A5I_ARATH	Serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' iota isoform (PP2A, B' subunit, ...	0.33	-	mit	0					500
O75716 UniProt NPD GO	STK16_HUMAN	Serine/threonine-protein kinase 16 (EC 2.7.11.1) (Protein kinase PKL12) (Myristoylated and palmitoyl ...	0.33	-	cyt	0	Membrane; lipid-anchor (Probable)		604719	2BUJ	304
Q9ZWC8 UniProt NPD GO	BRL1_ARATH	Serine/threonine-protein kinase BRI1-like 1 precursor (EC 2.7.11.1) (BRASSINOSTEROID INSENSITIVE 1-l ...	0.33	-	end	2 *	Cell membrane; single-pass type I membrane protein				1166
Q9U1Y5 UniProt NPD GO	CHK2_CAEEL	Serine/threonine-protein kinase chk-2 (EC 2.7.11.1) (Ce-cds-1) (Ce-chk-2)	0.33	-	mit	0	Nucleus				476
Q9UW86 UniProt NPD GO	PP1_NEUCR	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.33	-	cyt	0	Cytoplasm (By similarity)				308
Q20618 UniProt NPD GO	SRA13_CAEEL	Serpentine receptor class alpha-13 (Protein sra-13)	0.33	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				335
Q9UBL3 UniProt NPD GO	ASH2L_HUMAN	Set1/Ash2 histone methyltransferase complex subunit ASH2 (ASH2-like protein)	0.33	-	cyt	0	Nucleus (Probable)	nucleus [IDA]	604782		628
Q39012 UniProt NPD GO	KSG9_ARATH	Shaggy-related protein kinase iota (EC 2.7.11.1) (ASK-iota)	0.33	-	cyt	0					407
P01423 UniProt NPD GO	NXS2_NAJNI	Short neurotoxin 2 (Neurotoxin beta)	0.33	-	nuc	0	Secreted protein			1LNK	61
P25496 UniProt NPD GO	NXSB_LATCR	Short neurotoxin B	0.33	-	nuc	0	Secreted protein				62
Q64689 UniProt NPD GO	SIA8C_MOUSE	Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase (EC 2.4.99.-) (ST8 alpha-N-acetyl-ne ...	0.33	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				380
Q96PQ1 UniProt NPD GO	SIG12_HUMAN	Sialic acid-binding Ig-like lectin 12 precursor (Siglec-12) (Sialic acid-binding Ig-like lectin-like ...	0.33	-	exc	1	Membrane; single-pass type I membrane protein		606094		595
Q99PW5 UniProt NPD GO	NEUR3_RAT	Sialidase-3 (EC 3.2.1.18) (Membrane sialidase) (Ganglioside sialidase) (N-acetyl-alpha-neuraminidase ...	0.33	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				418
Q3T0M2 UniProt NPD GO	SFXN4_BOVIN	Sideroflexin-4	0.33	-	end	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				313
P49966 UniProt NPD GO	SR542_ARATH	Signal recognition particle 54 kDa protein 2 (SRP54)	0.33	-	cyt	0	Cytoplasm				495
P21565 UniProt NPD GO	SRP54_SCHPO	Signal recognition particle 54 kDa protein homolog (SRP54)	0.33	-	cyt	0	Cytoplasm	signal recognition particle (sensu Eukaryota) [TAS]			522
O13475 UniProt NPD GO	SEC65_KLULA	Signal recognition particle SEC65 subunit	0.33	-	nuc	0	Cytoplasm (By similarity)				270
O75886 UniProt NPD GO	STAM2_HUMAN	Signal transducing adapter molecule 2 (STAM-2)	0.33	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)		606244	1X5B	525
P27784 UniProt NPD GO	CCL6_MOUSE	Small inducible cytokine A6 precursor (CCL6) (C10 protein) [Contains: CCL6(22-95); CCL6(23-95)]	0.33	-	exc	1 *	Secreted protein				116
P97885 UniProt NPD GO	SCYB5_RAT	Small inducible cytokine B5 precursor (CXCL5) (Cytokine LIX)	0.33	-	mit	0	Secreted protein				130
Q9UHP9 UniProt NPD GO	SMPX_HUMAN	Small muscular protein (Stretch-responsive skeletal muscle protein)	0.33	-	nuc	0			300226		86
Q5RB90 UniProt NPD GO	SMPX_PONPY	Small muscular protein (Stretch-responsive skeletal muscle protein)	0.33	-	nuc	0					86
O70562 UniProt NPD GO	SPR2K_MOUSE	Small proline-rich protein 2K	0.33	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			68
Q6P4J8 UniProt NPD GO	SMU1_XENTR	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
O61365 UniProt NPD GO	NACH_DROME	Sodium channel protein Nach (Pickpocket 4)	0.33	-	end	2	Membrane; multi-pass membrane protein	integral to membrane [NAS]			535
P48764 UniProt NPD GO	SL9A3_HUMAN	Sodium/hydrogen exchanger 3 (Na(+)/H(+) exchanger 3) (NHE-3) (Solute carrier family 9 member 3)	0.33	+	end	12 *	Membrane; multi-pass membrane protein		182307		834
Q9UIG8 UniProt NPD GO	SO3A1_HUMAN	Solute carrier organic anion transporter family member 3A1 (Solute carrier family 21 member 11) (Sod ...	0.33	-	end	12 *	Membrane; multi-pass membrane protein				710
P37886 UniProt NPD GO	SOMA_MESAU	Somatotropin precursor (Growth hormone)	0.33	-	exc	0	Secreted protein				216
O62754 UniProt NPD GO	SOMA_TRIVU	Somatotropin precursor (Growth hormone)	0.33	-	exc	0	Secreted protein				215
Q5KF84 UniProt NPD GO	SNX3_CRYNE	Sorting nexin-3	0.33	-	mit	0	Cytoplasm (By similarity)				144
O62771 UniProt NPD GO	SP17_MONDO	Sperm surface protein Sp17 (Sperm autoantigenic protein 17)	0.33	+	nuc	0	Membrane; peripheral membrane protein (Potential)				179
Q86QI0 UniProt NPD GO	H1L2_OSTED	Sperm-specific H1/protamine-like protein type 2 precursor [Contains: Sperm-specific protein OE2 (Spe ...	0.33	-	nuc	0	Nucleus (By similarity)				126
Q08142 UniProt NPD GO	SMR1_PODAN	Sporulation minus regulator 1	0.33	-	nuc	0	Nucleus				356
P43648 UniProt NPD GO	STC_ONCMY	Stanniocalcin precursor (STC) (Corpuscles of Stannius protein) (CS) (Hypocalcin) (Teleocalcin)	0.33	-	cyt	0	Secreted protein				256
O76061 UniProt NPD GO	STC2_HUMAN	Stanniocalcin-2 precursor (STC-2) (Stanniocalcin-related protein) (STCRP) (STC-related protein)	0.33	-	exc	0	Secreted protein (Potential)		603665		302
Q9DG10 UniProt NPD GO	STAR_BRARE	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.33	-	cyt	0	Mitochondrion (By similarity)				285
Q9NRL3 UniProt NPD GO	STRN4_HUMAN	Striatin-4 (Zinedin)	0.33	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [TAS] membrane fraction [TAS]			753
P07152 UniProt NPD GO	MMP10_RAT	Stromelysin-2 precursor (EC 3.4.24.22) (Matrix metalloproteinase-10) (MMP-10) (Transin-2) (SL-2) (Tr ...	0.33	-	mit	0					476
Q29YR5 UniProt NPD GO	ST2B1_RAT	Sulfotransferase family cytosolic 2B member 1 (EC 2.8.2.2) (Sulfotransferase 2B1) (Sulfotransferase ...	0.33	-	nuc	0	Cytoplasm (By similarity)				340
P42285 UniProt NPD GO	SK2L2_HUMAN	Superkiller viralicidic activity 2-like 2 (EC 3.6.1.-) (ATP-dependent helicase SKIV2L2)	0.33	-	nuc	0	Nucleus; nucleolus				1042
P09925 UniProt NPD GO	SURF1_MOUSE	Surfeit locus protein 1	0.33	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				306
P34741 UniProt NPD GO	SDC2_HUMAN	Syndecan-2 precursor (SYND2) (Fibroglycan) (Heparan sulfate proteoglycan core protein) (HSPG)	0.33	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142460		201
Q64324 UniProt NPD GO	STXB2_MOUSE	Syntaxin-binding protein 2 (UNC-18 homolog 2) (UNC-18B) (MUSEC1)	0.33	-	cyt	0					593
P01736 UniProt NPD GO	TVB3_MOUSE	T-cell receptor beta chain V region PHDS203 precursor (Fragment)	0.33	-	cyt	0					120

You are viewing entries 38001 to 38050 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.