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
P94026 UniProt NPD GO	RBCMT_TOBAC	Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast precu ...	0.18	-	mit	0	Plastid; chloroplast				491
Q9UDX4 UniProt NPD GO	S14L3_HUMAN	SEC14-like protein 3 (Tocopherol-associated protein 2)	0.18	-	cyt	0					400
P92958 UniProt NPD GO	KIN11_ARATH	SNF1-related protein kinase catalytic subunit alpha KIN11 (EC 2.7.11.1) (AKIN11) (AKIN alpha1)	0.18	-	nuc	0					512
P40667 UniProt NPD GO	CH03_CHICK	SRY-related protein CH3 (Fragment)	0.18	-	nuc	0	Nucleus (Potential)				54
Q9H3S1 UniProt NPD GO	SEM4A_HUMAN	Semaphorin-4A precursor (Semaphorin B) (Sema B)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		607292		761
Q29538 UniProt NPD GO	RNS_SAITA	Seminal ribonuclease (EC 3.1.27.5) (Seminal RNase) (Fragment)	0.18	-	nuc	0	Secreted protein (By similarity)				104
Q80X76 UniProt NPD GO	SPA3F_MOUSE	Serine protease inhibitor A3F (Serpin A3F)	0.18	-	nuc	0					445
P09139 UniProt NPD GO	SPYA_RAT	Serine--pyruvate aminotransferase, mitochondrial precursor (EC 2.6.1.51) (SPT) (Alanine--glyoxylate ...	0.18	-	mit	0	Mitochondrion; mitochondrial matrix. Induced on glucagon administration. Peroxisome. Not effected by ...				414
P42818 UniProt NPD GO	KPK1_ARATH	Serine/threonine-protein kinase AtPK1/AtPK6 (EC 2.7.11.1)	0.18	-	mit	0					465
Q9YHZ5 UniProt NPD GO	PIM1_BRARE	Serine/threonine-protein kinase Pim-1 (EC 2.7.11.1)	0.18	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				310
Q5RF15 UniProt NPD GO	TNI3K_PONPY	Serine/threonine-protein kinase TNNI3K (EC 2.7.11.1) (TNNI3-interacting kinase)	0.18	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Expressed at lower levels in the cytoplasm (By s ...				617
O13958 UniProt NPD GO	PRK1_SCHPO	Serine/threonine-protein kinase prk1 (EC 2.7.11.22) (Suppressor of RNA polymerase B srb10)	0.18	-	cyt	0	Nucleus (Probable)				352
Q4I0M9 UniProt NPD GO	PTPA1_GIBZE	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				445
P48453 UniProt NPD GO	PP2BB_MOUSE	Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform (EC 3.1.3.16) (Calmodulin-dep ...	0.18	-	cyt	0					525
P20651 UniProt NPD GO	PP2BB_RAT	Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform (EC 3.1.3.16) (Calmodulin-dep ...	0.18	-	cyt	0					525
Q75D77 UniProt NPD GO	PP4R2_ASHGO	Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PP4R2)	0.18	-	cyt	0	Nucleus (By similarity)				356
Q9SJF0 UniProt NPD GO	BSL2_ARATH	Serine/threonine-protein phosphatase BSL2 (EC 3.1.3.16) (BSU1-like protein 2)	0.18	-	end	0	Nucleus (By similarity)				1088
P48578 UniProt NPD GO	PP2A4_ARATH	Serine/threonine-protein phosphatase PP2A-4 catalytic subunit (EC 3.1.3.16) (Protein phosphatase 2A ...	0.18	-	nuc	0	Cytoplasm				313
Q64666 UniProt NPD GO	SNAT_RAT	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.18	-	cyt	0					205
Q09203 UniProt NPD GO	SRA1_CAEEL	Serpentine receptor class alpha-1 (Protein sra-1)	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				331
Q10935 UniProt NPD GO	SRA33_CAEEL	Serpentine receptor class alpha-33 (Protein sra-33)	0.18	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				327
O01608 UniProt NPD GO	SRD32_CAEEL	Serpentine receptor class delta-32 (Protein srd-32)	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				339
P46566 UniProt NPD GO	SRG9_CAEEL	Serpentine receptor class gamma-9 (Protein srg-9)	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				336
O35090 UniProt NPD GO	ALBU_MERUN	Serum albumin precursor	0.18	-	exc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			609
P02770 UniProt NPD GO	ALBU_RAT	Serum albumin precursor	0.18	-	exc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			608
P81491 UniProt NPD GO	SAA5_MESAU	Serum amyloid A-5 protein	0.18	-	cyt	0					102
P19958 UniProt NPD GO	NXS3_AIPLA	Short neurotoxin C	0.18	-	nuc	0	Secreted protein				60
P70122 UniProt NPD GO	SBDS_MOUSE	Shwachman-Bodian-Diamond syndrome protein homolog (Protein 22A3)	0.18	-	cyt	0					249
Q8BZL1 UniProt NPD GO	NEUR4_MOUSE	Sialidase-4 (EC 3.2.1.18) (Neuraminidase 4) (N-acetyl-alpha-neuraminidase 4)	0.18	-	cyt	0	Membrane; peripheral membrane protein (By similarity)	lysosome [ISS] organelle inner membrane [ISS]			501
Q59I47 UniProt NPD GO	SMUG1_BOVIN	Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-)	0.18	-	cyt	0	Nucleus (By similarity)	nucleolus [ISS]			272
Q04837 UniProt NPD GO	SSB_HUMAN	Single-stranded DNA-binding protein, mitochondrial precursor (Mt-SSB) (MtSSB) (PWP1-interacting prot ...	0.18	-	mit	0	Mitochondrion		600439	3ULL	148
P13673 UniProt NPD GO	SKGR_XENLA	Skin granule protein precursor	0.18	-	exc	0	Secreted protein				213
P61274 UniProt NPD GO	CCL2_MACFA	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.18	-	exc	0	Secreted protein				99
P61275 UniProt NPD GO	CCL2_MACMU	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.18	-	exc	0	Secreted protein				99
P55773 UniProt NPD GO	CCL23_HUMAN	Small inducible cytokine A23 precursor (CCL23) (Macrophage inflammatory protein 3) (MIP-3) (Myeloid ...	0.18	-	exc	0	Secreted protein		602494	1G91	120
P62318 UniProt NPD GO	SMD3_HUMAN	Small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3)	0.18	+	nuc	0	Nucleus		601062	1D3B	126
P62320 UniProt NPD GO	SMD3_MOUSE	Small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3)	0.18	+	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			126
P62323 UniProt NPD GO	SMD3_XENLA	Small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3)	0.18	+	nuc	0	Nucleus (By similarity)				126
O70554 UniProt NPD GO	SPR2B_MOUSE	Small proline-rich protein 2B	0.18	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			98
Q07699 UniProt NPD GO	SCN1B_HUMAN	Sodium channel beta-1 subunit precursor	0.18	-	end	1	Membrane; single-pass type I membrane protein		604233		218
P97952 UniProt NPD GO	SCN1B_MOUSE	Sodium channel beta-1 subunit precursor	0.18	-	end	1	Membrane; single-pass type I membrane protein				218
P53788 UniProt NPD GO	SCN1B_RABIT	Sodium channel beta-1 subunit precursor	0.18	-	end	1	Membrane; single-pass type I membrane protein				218
Q00954 UniProt NPD GO	SCN1B_RAT	Sodium channel beta-1 subunit precursor	0.18	-	end	1	Membrane; single-pass type I membrane protein				218
Q96N87 UniProt NPD GO	S6A18_HUMAN	Sodium- and chloride-dependent transporter XTRP2 (Solute carrier family 6 member 18)	0.18	-	end	13 *	Membrane; multi-pass membrane protein (Probable)				628
Q5R9L5 UniProt NPD GO	S20A1_PONPY	Sodium-dependent phosphate transporter 1 (Solute carrier family 20 member 1)	0.18	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				679
Q61165 UniProt NPD GO	SL9A1_MOUSE	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1)	0.18	-	end	12 *	Membrane; multi-pass membrane protein	basolateral plasma membrane [TAS] membrane fraction [IDA]			820
P26431 UniProt NPD GO	SL9A1_RAT	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1)	0.18	-	end	13 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			820
P19634 UniProt NPD GO	SL9A1_HUMAN	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1) (Na( ...	0.18	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	107310	1Y4E	815
P55013 UniProt NPD GO	S12A2_SQUAC	Solute carrier family 12 member 2 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1) ...	0.18	-	end	12	Membrane; multi-pass membrane protein				1191
Q27994 UniProt NPD GO	GTR4_BOVIN	Solute carrier family 2, facilitated glucose transporter member 4 (Glucose transporter type 4, insul ...	0.18	-	end	11 *	Intracytoplasmic membrane; perinuclear region; multi-pass membrane protein (By similarity). Localize ...				509

You are viewing entries 53651 to 53700 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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