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
Q10041 UniProt NPD GO	YRC2_CAEEL	Hypothetical protein K01A12.2	0.51	-	mit	0					89
P34664 UniProt NPD GO	YOY6_CAEEL	Hypothetical protein ZK652.6	0.51	-	nuc	0	Nucleus (Potential)				575
O94497 UniProt NPD GO	YBS7_SCHPO	Hypothetical serine-rich protein C18E5.07 in chromosome II	0.51	-	nuc	0					615
Q4HTS9 UniProt NPD GO	ISN1_GIBZE	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.51	-	mit	0					430
Q6CY84 UniProt NPD GO	ISN1_KLULA	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.51	-	nuc	0					422
Q63ZW7 UniProt NPD GO	INADL_MOUSE	InaD-like protein (Inadl protein) (Pals1-associated tight junction protein) (Protein associated to t ...	0.51	-	nuc	0	Cell membrane; cell-cell junction; tight junction; peripheral membrane protein. Localizes to tight j ...	apical part of cell [IDA]			1834
Q8C0D7 UniProt NPD GO	ING4_MOUSE	Inhibitor of growth protein 4 (p29ING4)	0.51	-	nuc	0	Nucleus (By similarity)			1WEU	249
P22817 UniProt NPD GO	IDE_DROME	Insulin-degrading enzyme (EC 3.4.24.56) (Insulysin) (Insulinase) (Insulin protease)	0.51	-	pox	0					989
P05019 UniProt NPD GO	IGF1B_HUMAN	Insulin-like growth factor IB precursor (IGF-IB) (Somatomedin C) (Mechano growth factor) (MGF)	0.51	-	nuc	0	Secreted protein		147440	3LRI	195
Q68FR3 UniProt NPD GO	PHF22_RAT	Integrator complex subunit 12 (PHD finger protein 22)	0.51	-	nuc	0					461
Q64632 UniProt NPD GO	ITB4_RAT	Integrin beta-4 precursor (GP150) (CD104 antigen)	0.51	-	exc	2	Membrane; single-pass type I membrane protein	cytoplasm [TAS] extracellular space [TAS] integral to membrane [TAS] integrin complex [TAS]			1807
P01569 UniProt NPD GO	IFNA5_HUMAN	Interferon alpha-5 precursor (Interferon alpha-G) (LeIF G) (Interferon alpha-61)	0.51	-	vac	0	Secreted protein		147565		189
Q15306 UniProt NPD GO	IRF4_HUMAN	Interferon regulatory factor 4 (IRF-4) (Lymphocyte-specific interferon regulatory factor) (LSIRF) (N ...	0.51	-	nuc	0	Nucleus	nucleus [IC]	601900		451
Q9NPH9 UniProt NPD GO	IL26_HUMAN	Interleukin-26 precursor (AK155 protein)	0.51	-	mit	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	605679		171
Q5WN60 UniProt NPD GO	IFC2_CAEBR	Intermediate filament protein ifc-2	0.51	-	cyt	0	Cytoplasm (By similarity)				621
P36046 UniProt NPD GO	MIA40_YEAST	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.51	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...	mitochondrial inner membrane [IDA] mitochondrial intermembrane space [IDA] mitochondrion [IDA]			403
Q9W0K0 UniProt NPD GO	JIP1_DROME	JNK-interacting protein 1 (JIP-1) (Protein eye developmental SP512) (APP-like-interacting protein 1) ...	0.51	-	nuc	0	Cytoplasm (Probable)				490
Q75AL5 UniProt NPD GO	JHD1_ASHGO	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.51	+	cyt	0	Nucleus (By similarity)				486
Q9SEX2 UniProt NPD GO	KTNA1_ARATH	Katanin p60 ATPase-containing subunit (EC 3.6.4.3) (Katanin p60 subunit) (p60 katanin) (Atp60) (CAD ...	0.51	-	nuc	0					523
Q9R0H5 UniProt NPD GO	K2C6G_MOUSE	Keratin, type II cytoskeletal 6G (Cytokeratin-6G) (CK 6G) (K6g keratin) (Keratin-K6irs) (mK6irs1/Krt ...	0.51	-	nuc	0		intermediate filament [ISS]			524
Q10758 UniProt NPD GO	K2C8_RAT	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8) (Cytokeratin endo A)	0.51	-	mit	0	Cytoplasm. Nucleus; nucleoplasm; nuclear matrix	dystrophin-associated glycoprotein complex [IDA] sarcolemma [IDA] Z disc [IDA]			482
Q9BYQ5 UniProt NPD GO	KR415_HUMAN	Keratin-associated protein 4-15 (Keratin-associated protein 4.15) (Ultrahigh sulfur keratin-associat ...	0.51	-	mit	0					193
Q2TBQ9 UniProt NPD GO	KLC3_BOVIN	Kinesin light chain 3	0.51	-	nuc	0	Elongating spermatid tail midpiece, localized in outer dense fibers (ODFs) and associates with mitoc ...				505
Q13886 UniProt NPD GO	KLF9_HUMAN	Krueppel-like factor 9 (Transcription factor BTEB1) (Basic transcription element-binding protein 1) ...	0.51	-	nuc	0	Nucleus		602902		244
P43603 UniProt NPD GO	LSB3_YEAST	LAS seventeen-binding protein 3 (LAS17-binding protein 3)	0.51	-	nuc	0	Cytoplasm	bud neck [IDA] cytoplasm [IDA] mitochondrion [IDA]		1SSH	451
Q9UBR4 UniProt NPD GO	LHX3_HUMAN	LIM/homeobox protein Lhx3	0.51	+	nuc	0	Nucleus (Probable)	nucleus [TAS]	600577		397
P50481 UniProt NPD GO	LHX3_MOUSE	LIM/homeobox protein Lhx3 (Homeobox protein LIM-3) (Homeobox protein P-LIM) (LIM homeobox protein 3) ...	0.51	+	nuc	0	Nucleus (Probable)				400
P80025 UniProt NPD GO	PERL_BOVIN	Lactoperoxidase precursor (EC 1.11.1.7) (LPO)	0.51	-	exc	0	Secreted protein; extracellular space				712
Q5T752 UniProt NPD GO	LCE1D_HUMAN	Late cornified envelope protein 1D (Late envelope protein 4)	0.51	-	mit	0					114
O14633 UniProt NPD GO	LCE2B_HUMAN	Late cornified envelope protein 2B (Late envelope protein 10) (Small proline-rich-like epidermal dif ...	0.51	-	nuc	0					110
Q14767 UniProt NPD GO	LTBP2_HUMAN	Latent-transforming growth factor beta-binding protein 2 precursor (LTBP-2)	0.51	-	nuc	0	Secreted protein (By similarity). Localized in nuchal ligament and aorta to the fibrillin-containing ...	extracellular matrix (sensu Metazoa) [TAS]	602091		1821
Q3TJ91 UniProt NPD GO	L2GL2_MOUSE	Lethal(2) giant larvae protein homolog 2 (Lethal giant larvae-like protein 2)	0.51	-	nuc	0	Cytoplasm. Localized in the perinuclear structure and faintly at the cell-cell contacts sites in the ...				1027
Q4P4G2 UniProt NPD GO	LCMT1_USTMA	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.51	-	nuc	0					536
Q9P3K9 UniProt NPD GO	LCMT2_NEUCR	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.51	+	cyt	0					1213
Q8TF66 UniProt NPD GO	LRC15_HUMAN	Leucine-rich repeat-containing protein 15 precursor (hLib)	0.51	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				581
P13838 UniProt NPD GO	LEUK_RAT	Leukosialin precursor (Leukocyte sialoglycoprotein) (Sialophorin) (W3/13 antigen) (CD43 antigen) (Fr ...	0.51	+	nuc	1	Membrane; single-pass type I membrane protein				378
P26156 UniProt NPD GO	CHLN_MARPO	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.51	+	cyt	0	Plastid; chloroplast				465
P35952 UniProt NPD GO	LDLR_RAT	Low-density lipoprotein receptor precursor (LDL receptor)	0.51	-	exc	1	Membrane; single-pass type I membrane protein				879
Q8BUJ9 UniProt NPD GO	LRP12_MOUSE	Low-density lipoprotein receptor-related protein 12 precursor	0.51	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)				858
Q9Y561 UniProt NPD GO	LRP12_HUMAN	Low-density lipoprotein receptor-related protein 12 precursor (Suppressor of tumorigenicity protein ...	0.51	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [IEP] membrane fraction [IEP]			859
Q9HD23 UniProt NPD GO	MRS2L_HUMAN	Magnesium transporter MRS2L, mitochondrial precursor (MRS2-like protein)	0.51	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				443
Q9R0S3 UniProt NPD GO	MMP17_MOUSE	Matrix metalloproteinase-17 precursor (EC 3.4.24.-) (MMP-17) (Membrane-type matrix metalloproteinase ...	0.51	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				578
Q52TG9 UniProt NPD GO	MATK_CARMI	Maturase K (Intron maturase)	0.51	-	nuc	0	Plastid; chloroplast				517
Q85V94 UniProt NPD GO	MATK_ELAUM	Maturase K (Intron maturase)	0.51	-	cyt	0	Plastid; chloroplast				505
Q95BX9 UniProt NPD GO	MATK_HUMLU	Maturase K (Intron maturase)	0.51	-	cyt	0	Plastid; chloroplast				507
Q9GIH9 UniProt NPD GO	MATK_LILHE	Maturase K (Intron maturase)	0.51	-	cyt	1	Plastid; chloroplast				512
Q8MCN7 UniProt NPD GO	MATK_TRIBU	Maturase K (Intron maturase)	0.51	-	cyt	0	Plastid; chloroplast				511
Q9XPP8 UniProt NPD GO	MATK_TRIUN	Maturase K (Intron maturase)	0.51	-	cyt	0	Plastid; chloroplast				515
P83084 UniProt NPD GO	M5H41_BOMMX	Maximins 5/H4 type 1 precursor [Contains: Maximin-5; Maximin-H4]	0.51	-	end	0	Secreted protein				145
Q9VBQ9 UniProt NPD GO	MED28_DROME	Mediator of RNA polymerase II transcription subunit 28 (Mediator complex subunit 28) (Med23 homolog) ...	0.51	-	nuc	0	Nucleus (Probable)	mediator complex [IPI]			189

You are viewing entries 24401 to 24450 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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