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
Q41005 UniProt NPD GO	CBPX_PEA	Serine carboxypeptidase-like (EC 3.4.16.-) (Fragment)	0.01	-	cyt	0					286
P49357 UniProt NPD GO	GLYM_FLAPR	Serine hydroxymethyltransferase 1, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine ...	0.01	-	mit	0	Mitochondrion				517
P49358 UniProt NPD GO	GLYN_FLAPR	Serine hydroxymethyltransferase 2, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine ...	0.01	-	mit	0	Mitochondrion				517
P50433 UniProt NPD GO	GLYM_SOLTU	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.01	-	cyt	0	Mitochondrion				518
Q750C9 UniProt NPD GO	TSC3_ASHGO	Serine palmitoyltransferase-regulating protein TSC3	0.01	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				107
Q6CJH4 UniProt NPD GO	TSC3_KLULA	Serine palmitoyltransferase-regulating protein TSC3	0.01	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				84
P24743 UniProt NPD GO	SPI8_SOLTU	Serine protease inhibitor 8 (PKI-1) (Fragment)	0.01	-	cyt	0					42
P37109 UniProt NPD GO	ISK4_PIG	Serine protease inhibitor Kazal-type 4 precursor (Peptide PEC-60)	0.01	-	mit	0	Secreted protein			1PCE	86
Q6UWN8 UniProt NPD GO	ISK6_HUMAN	Serine protease inhibitor Kazal-type 6 precursor	0.01	-	exc	1 *	Secreted protein (Potential)				80
P58062 UniProt NPD GO	ISK7_HUMAN	Serine protease inhibitor Kazal-type 7 precursor (Esophagus cancer-related gene 2 protein) (ECRG-2)	0.01	-	exc	0	Secreted protein (Potential)				85
Q6IE32 UniProt NPD GO	ISK7_MOUSE	Serine protease inhibitor Kazal-type 7 precursor (Esophagus cancer-related gene 2 protein) (ECRG-2)	0.01	-	end	0	Secreted protein (Potential)				76
Q6IE51 UniProt NPD GO	ISK7_RAT	Serine protease inhibitor Kazal-type 7 precursor (Esophagus cancer-related gene 2 protein) (ECRG-2)	0.01	-	vac	0	Secreted protein (Potential)				74
O96790 UniProt NPD GO	DPGN_DIPMA	Serine protease inhibitor dipetalogastin precursor (Dipetalin) (Fragment)	0.01	-	nuc	0	Secreted protein			1KMA	351
Q8AX01 UniProt NPD GO	MOS_DENAN	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.01	-	cyt	0					194
O36016 UniProt NPD GO	PTPA1_SCHPO	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				325
Q6C712 UniProt NPD GO	PTPA2_YARLI	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.01	-	nuc	0	Cytoplasm (By similarity)				354
Q27884 UniProt NPD GO	PPV_DROME	Serine/threonine-protein phosphatase PP-V (EC 3.1.3.16)	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]			303
P40585 UniProt NPD GO	PAU15_YEAST	Seripauperin-15 precursor	0.01	-	cyt	0					124
Q12370 UniProt NPD GO	PAU17_YEAST	Seripauperin-17 precursor	0.01	-	cyt	0					124
P42221 UniProt NPD GO	PAU19_YEAST	Seripauperin-19/21/22 precursor	0.01	-	cyt	0					124
P25610 UniProt NPD GO	PAU3_YEAST	Seripauperin-3	0.01	-	cyt	1 *					124
P46501 UniProt NPD GO	SRB10_CAEEL	Serpentine receptor class beta-10 (Protein srb-10)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				185
O01509 UniProt NPD GO	SRB15_CAEEL	Serpentine receptor class beta-15 (Protein srb-15)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				336
P92001 UniProt NPD GO	SRD18_CAEEL	Serpentine receptor class delta-18 (Protein srd-18)	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				337
P91211 UniProt NPD GO	SRD31_CAEEL	Serpentine receptor class delta-31 (Protein srd-31)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				315
Q19258 UniProt NPD GO	SRG69_CAEEL	Serpentine receptor class gamma-69 (Protein srg-69)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				342
P35237 UniProt NPD GO	SPB6_HUMAN	Serpin B6 (Placental thrombin inhibitor) (Cytoplasmic antiproteinase) (CAP) (Protease inhibitor 6) ( ...	0.01	-	cyt	0	Cytoplasm	cytosol [TAS]	173321		376
Q60854 UniProt NPD GO	SPB6_MOUSE	Serpin B6 (Placental thrombin inhibitor) (Protease inhibitor 6) (PI-6)	0.01	-	mit	0	Cytoplasm			1M37	378
O19063 UniProt NPD GO	SAMP_PIG	Serum amyloid P-component precursor (SAP)	0.01	-	exc	0	Secreted protein				224
P27170 UniProt NPD GO	PON1_RABIT	Serum paraoxonase/arylesterase 1 (EC 3.1.1.2) (EC 3.1.8.1) (PON 1) (Serum aryldialkylphosphatase 1) ...	0.01	-	cyt	0	Secreted protein; extracellular space	extracellular region [NAS]		1V04	358
P27169 UniProt NPD GO	PON1_HUMAN	Serum paraoxonase/arylesterase 1 (EC 3.1.1.2) (EC 3.1.8.1) (PON 1) (Serum aryldialkylphosphatase 1) ...	0.01	-	mit	0	Secreted protein; extracellular space	extracellular region [NAS]	168820	1V04	354
Q58DS7 UniProt NPD GO	PON2_BOVIN	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.01	-	mit	0	Membrane; peripheral membrane protein (By similarity)				354
P54832 UniProt NPD GO	PON2_CANFA	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.01	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				354
Q90952 UniProt NPD GO	PON2_CHICK	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.01	-	mit	0	Membrane; peripheral membrane protein (By similarity)				354
Q6AXM8 UniProt NPD GO	PON2_RAT	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.01	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				354
Q15166 UniProt NPD GO	PON3_HUMAN	Serum paraoxonase/lactonase 3 (EC 3.1.1.-)	0.01	-	end	1 *	Secreted protein; extracellular space (By similarity)	extracellular region [NAS]	602720		354
Q68FP2 UniProt NPD GO	PON3_RAT	Serum paraoxonase/lactonase 3 (EC 3.1.1.-)	0.01	-	end	0	Secreted protein; extracellular space (By similarity)				354
Q9US59 UniProt NPD GO	SKB5_SCHPO	Shk1 kinase-binding protein 5	0.01	-	cyt	0					140
Q9W7K1 UniProt NPD GO	NXS2_PSETE	Short neurotoxin 2 precursor (Alpha neurotoxin 2)	0.01	-	mit	0	Secreted protein (By similarity)				79
P59072 UniProt NPD GO	NXSN1_PSETE	Short neurotoxin N1 (Alpha neurotoxin) (Fragment)	0.01	-		0	Secreted protein				11
P59073 UniProt NPD GO	NXSN2_PSETE	Short neurotoxin N2 (Alpha neurotoxin) (Fragment)	0.01	-		0	Secreted protein				15
Q9MYW0 UniProt NPD GO	TRPC6_BOVIN	Short transient receptor potential channel 6 (TrpC6) (Fragment)	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Probable)				89
Q08632 UniProt NPD GO	SDR1_PICAB	Short-chain type dehydrogenase/reductase (EC 1.-.-.-)	0.01	-	cyt	0					271
P82450 UniProt NPD GO	SIAE_RAT	Sialate o-acetylesterase (EC 3.1.1.53) (Sialic acid-specific 9-O-acetylesterase) (Fragments)	0.01	-	cyt	1 *	Lysosome				58
P18271 UniProt NPD GO	8513_TRYCR	Sialidase 85-1.3 (EC 3.2.1.18) (Neuraminidase) (NA) (Major 85 kDa surface antigen) (SA85-1.3 protein ...	0.01	-	cyt	0					175
P42634 UniProt NPD GO	TKS1_AEDAE	Sialokinin-1 (Sialokinin I)	0.01	-		0	Secreted protein				10
P42635 UniProt NPD GO	TKS2_AEDAE	Sialokinin-2 (Sialokinin II)	0.01	-		0	Secreted protein				10
Q870L2 UniProt NPD GO	MIRB_EMENI	Siderophore iron transporter mirB (Major facilitator iron-regulated transporter B) (Triacetylfusarin ...	0.01	-	end	14	Membrane; multi-pass membrane protein (Potential)				604
Q3SZU5 UniProt NPD GO	SPCS3_BOVIN	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 (Potential)				180
P61008 UniProt NPD GO	SPCS3_CANFA	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				180

You are viewing entries 91451 to 91500 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.