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
Q8NC54 UniProt NPD GO	KCT2_HUMAN	Keratinocytes-associated transmembrane protein 2 precursor	0.62	-	mit	1 *	Membrane; single-pass type I membrane protein (Potential)				265
Q10198 UniProt NPD GO	NDC80_SCHPO	Kinetochore protein ndc80	0.62	-	nuc	0	Nucleus. Associated with kinetochores	Ndc80 complex [TAS]			624
Q60843 UniProt NPD GO	KLF2_MOUSE	Krueppel-like factor 2 (Lung krueppel-like factor)	0.62	-	nuc	0	Nucleus (By similarity)				354
Q9ET58 UniProt NPD GO	KLF2_RAT	Krueppel-like factor 2 (Lung krueppel-like factor)	0.62	-	nuc	0	Nucleus (By similarity)				351
O08584 UniProt NPD GO	KLF6_MOUSE	Krueppel-like factor 6 (Core promoter element-binding protein)	0.62	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			283
Q8MLV1 UniProt NPD GO	LBR_DROME	Lamin-B receptor (dLBR)	0.62	-	end	8	Nucleus; nuclear inner membrane; multi-pass membrane protein; nucleoplasmic side	integral to nuclear inner membrane [IDA] nuclear inner membrane [IDA]			741
P55268 UniProt NPD GO	LAMB2_HUMAN	Laminin beta-2 chain precursor (S-laminin) (Laminin B1s chain)	0.62	-	nuc	0	Secreted protein; extracellular space. S-laminin is concentrated in the synaptic cleft of the neurom ...	basal lamina [TAS]	150325		1798
P02468 UniProt NPD GO	LAMC1_MOUSE	Laminin gamma-1 chain precursor (Laminin B2 chain)	0.62	-	nuc	0	Secreted protein; extracellular space	basement membrane [IDA] laminin-1 [ISS]		1TLE	1607
Q61092 UniProt NPD GO	LAMC2_MOUSE	Laminin gamma-2 chain precursor (Laminin 5 gamma 2 subunit) (Kalinin/nicein/epiligrin 100 kDa subuni ...	0.62	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [IDA]			1191
Q13753 UniProt NPD GO	LAMC2_HUMAN	Laminin gamma-2 chain precursor (Laminin 5 gamma 2 subunit) (Kalinin/nicein/epiligrin 100 kDa subuni ...	0.62	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component		226700		1193
Q28019 UniProt NPD GO	LTBP2_BOVIN	Latent-transforming growth factor beta-binding protein 2 precursor (LTBP-2)	0.62	-	mit	0	Localized in nuchal ligament and aorta to the fibrillin-containing, microfibrillar component of elas ...				1842
O75096 UniProt NPD GO	LRP4_HUMAN	Low-density lipoprotein receptor-related protein 4 precursor (Multiple epidermal growth factor-like ...	0.62	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)		604270		1950
Q98931 UniProt NPD GO	LRP8_CHICK	Low-density lipoprotein receptor-related protein 8 precursor (Apolipoprotein E receptor 2) (LR8B pro ...	0.62	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				917
O88910 UniProt NPD GO	MPP3_MOUSE	MAGUK p55 subfamily member 3 (Protein MPP3) (Dlgh3 protein)	0.62	-	cyt	0					568
O54992 UniProt NPD GO	MAPK5_MOUSE	MAP kinase-activated protein kinase 5 (EC 2.7.11.1) (MAPK-activated protein kinase 5) (MAPKAP kinase ...	0.62	+	cyt	0	Cytoplasm (Probable). Nucleus (By similarity). Also observed in the nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			473
Q8N119 UniProt NPD GO	MMP21_HUMAN	Matrix metalloproteinase-21 precursor (EC 3.4.24.-) (MMP-21)	0.62	-	exc	0	Secreted protein (Potential)		608416		569
Q8SEL8 UniProt NPD GO	MATK_ACEMO	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				514
Q7HKI3 UniProt NPD GO	MATK_ACEOP	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				514
P30071 UniProt NPD GO	MATK_EPIVI	Maturase K (Intron maturase)	0.62	-	nuc	1 *	Plastid				439
Q5YK33 UniProt NPD GO	MATK_ERYCG	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				504
Q5GF67 UniProt NPD GO	MATK_IRICR	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				520
Q9G0R3 UniProt NPD GO	MATK_LIQST	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				503
Q8MEX7 UniProt NPD GO	MATK_MACCO	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				499
Q8MCP6 UniProt NPD GO	MATK_MEDTR	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				506
Q3T8Q6 UniProt NPD GO	MATK_MICCM	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				507
Q75VB4 UniProt NPD GO	MATK_QUECO	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				504
Q75VB2 UniProt NPD GO	MATK_QUEIL	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				504
Q5J2V4 UniProt NPD GO	MATK_SIMCH	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				504
Q8MCN9 UniProt NPD GO	MATK_TRIAO	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				506
Q8MCK8 UniProt NPD GO	MATK_TRIFG	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				506
Q8MCN2 UniProt NPD GO	MATK_TRIGC	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				506
Q8MCN0 UniProt NPD GO	MATK_TRIHY	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				506
Q8MCN8 UniProt NPD GO	MATK_TRIRS	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				506
Q8MCM0 UniProt NPD GO	MATK_TRISU	Maturase K (Intron maturase)	0.62	-	nuc	0	Plastid; chloroplast				506
Q6JVN2 UniProt NPD GO	MATK_WOLBI	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				504
Q76MH9 UniProt NPD GO	MATK_ZINMI	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				515
Q76MH8 UniProt NPD GO	MATK_ZINOF	Maturase K (Intron maturase)	0.62	-	cyt	0	Plastid; chloroplast				515
Q5SW45 UniProt NPD GO	MKS1_MOUSE	Meckel syndrome type 1 protein homolog	0.62	-	cyt	0					561
O94756 UniProt NPD GO	MEU14_SCHPO	Meiotic expression up-regulated protein 14	0.62	-	nuc	0	Nucleus; nuclear membrane; spindle pole body; cytoplasmic side. Forespore; forespore membrane				335
Q8R001 UniProt NPD GO	MARE2_MOUSE	Microtubule-associated protein RP/EB family member 2 (APC-binding protein EB2) (End-binding protein ...	0.62	-	nuc	0	Cytoplasm (By similarity). Associated with the microtubule network. Accumulates at the plus end of m ...				326
Q9T041 UniProt NPD GO	MAPT_ARATH	Microtubule-associated protein TORTIFOLIA1 (Microtubule-associated protein SPIRAL2) (Protein CONVOLU ...	0.62	-	mit	0	Cytoplasm. Bound to microtubules				864
P82921 UniProt NPD GO	RT21_HUMAN	Mitochondrial 28S ribosomal protein S21 (S21mt) (MRP-S21)	0.62	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			87
Q9CPV3 UniProt NPD GO	RT32_MOUSE	Mitochondrial 28S ribosomal protein S32 (S32mt) (MRP-S32)	0.62	-	nuc	0	Mitochondrion				142
Q6C2J1 UniProt NPD GO	GEM1_YARLI	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.62	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				665
Q02888 UniProt NPD GO	FMP14_YEAST	Mitochondrial protein FMP14 (Found in mitochondrial proteome protein 14)	0.62	-	mit	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			182
P46758 UniProt NPD GO	RT11_ACACA	Mitochondrial ribosomal protein S11	0.62	+	nuc	0	Mitochondrion				173
Q8RXG3 UniProt NPD GO	M2K5_ARATH	Mitogen-activated protein kinase kinase 5 (EC 2.7.12.2) (MAP kinase kinase 5) (AtMKK5) (AtMAP2Kalpha ...	0.62	-	exc	0					348
Q9P7Q8 UniProt NPD GO	PMO25_SCHPO	Mo25-like protein	0.62	-	cyt	0		contractile ring (sensu Fungi) [IDA] cytoplasm [IDA] medial ring [IDA] nucleus [IDA] spindle pole body [IDA]			329
Q9R1V3 UniProt NPD GO	SMAD5_RAT	Mothers against decapentaplegic homolog 5 (SMAD 5) (Mothers against DPP homolog 5) (Smad5)	0.62	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	integral to membrane [ISS] intracellular [ISS] nucleus [ISS]			465
Q9W734 UniProt NPD GO	SMAD6_CHICK	Mothers against decapentaplegic homolog 6 (SMAD 6) (Mothers against DPP homolog 6) (Smad6)	0.62	-	nuc	0					431

You are viewing entries 18001 to 18050 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.