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
Q9Y6N6 UniProt NPD GO	LAMC3_HUMAN	Laminin gamma-3 chain precursor (Laminin 12 gamma 3 subunit)	0.82	-	exc	0	Secreted protein; extracellular space	extracellular matrix (sensu Metazoa) [TAS] membrane [TAS]	604349		1587
O60309 UniProt NPD GO	LR37A_HUMAN	Leucine-rich repeat-containing protein 37A	0.82	-	nuc	1					1634
Q6NWG1 UniProt NPD GO	LRC59_BRARE	Leucine-rich repeat-containing protein 59	0.82	+	nuc	1	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				314
Q6NX28 UniProt NPD GO	LRC59_XENTR	Leucine-rich repeat-containing protein 59	0.82	+	nuc	1	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				308
Q99091 UniProt NPD GO	CPRF3_PETCR	Light-inducible protein CPRF-3	0.82	+	nuc	0	Nucleus				296
P42284 UniProt NPD GO	LOLA2_DROME	Longitudinals lacking protein, isoforms H/M/V	0.82	-	cyt	1	Nucleus	nucleus [IDA]			549
Q12912 UniProt NPD GO	LRMP_HUMAN	Lymphoid-restricted membrane protein (Protein Jaw1)	0.82	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...	endoplasmic reticulum membrane [TAS] integral to plasma membrane [TAS]	602003		555
Q10407 UniProt NPD GO	MKH1_SCHPO	MAP kinase kinase kinase mkh1 (EC 2.7.11.25)	0.82	-	nuc	0		cell septum [IDA] cytoplasm [IDA]			1116
P27448 UniProt NPD GO	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3 (EC 2.7.11.1) (Cdc25C-associated protein kinase 1) (cTA ...	0.82	-	nuc	0			602678		776
Q8K1K9 UniProt NPD GO	MIZF_MOUSE	MBD2-interacting zinc finger protein (Methyl-CpG-binding protein 2-interacting zinc finger protein)	0.82	-	nuc	0	Nucleus (By similarity)				503
Q6GL69 UniProt NPD GO	MK67I_XENTR	MKI67 FHA domain-interacting nucleolar phosphoprotein-like	0.82	-	nuc	0	Nucleus; nucleolus (By similarity)				276
Q969V6 UniProt NPD GO	MKL1_HUMAN	MKL/myocardin-like protein 1 (Myocardin-related transcription factor A) (MRTF-A) (Megakaryoblastic l ...	0.82	-	nuc	0	Nucleus (By similarity)		606078		931
Q8IZL2 UniProt NPD GO	MAML2_HUMAN	Mastermind-like protein 2 (Mam-2)	0.82	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate manner	nucleus [IDA]	607537		1153
P22016 UniProt NPD GO	B2_USTMA	Mating-type locus allele B2 protein	0.82	-	nuc	0	Nucleus				410
P22021 UniProt NPD GO	B7_USTMA	Mating-type locus allele B7 protein	0.82	+	nuc	0	Nucleus				410
Q9MUZ1 UniProt NPD GO	MATK_BRASY	Maturase K (Intron maturase)	0.82	+	cyt	0	Plastid; chloroplast				511
Q5GAA8 UniProt NPD GO	MATK_CRAPL	Maturase K (Intron maturase)	0.82	-	cyt	0	Plastid; chloroplast				507
Q9TIB6 UniProt NPD GO	MATK_ELEIN	Maturase K (Intron maturase)	0.82	+	nuc	0	Plastid; chloroplast				513
Q8MEX2 UniProt NPD GO	MATK_GINBI	Maturase K (Intron maturase)	0.82	-	nuc	0	Plastid; chloroplast				512
Q9TIR9 UniProt NPD GO	MATK_KIGAF	Maturase K (Intron maturase)	0.82	-	pox	0	Plastid; chloroplast				509
Q8MD24 UniProt NPD GO	MATK_LOACH	Maturase K (Intron maturase)	0.82	-	cyt	0	Plastid; chloroplast				508
Q8MD32 UniProt NPD GO	MATK_MENLA	Maturase K (Intron maturase)	0.82	-	cyt	0	Plastid; chloroplast				504
O46993 UniProt NPD GO	MATK_PAESU	Maturase K (Intron maturase)	0.82	-	nuc	0	Plastid; chloroplast				496
Q85ZS6 UniProt NPD GO	MATK_PSAJU	Maturase K (Intron maturase)	0.82	-	cyt	0	Plastid; chloroplast				511
Q8MCM4 UniProt NPD GO	MATK_TRIRP	Maturase K (Intron maturase)	0.82	-	nuc	0	Plastid; chloroplast				506
P04932 UniProt NPD GO	MSP1_PLAFK	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (P190)	0.82	+	exc	1	Cell membrane; lipid-anchor; GPI-anchor				1630
P55081 UniProt NPD GO	MFAP1_HUMAN	Microfibrillar-associated protein 1	0.82	-	nuc	0	Secreted protein; extracellular space; extracellular matrix		600215		439
P55080 UniProt NPD GO	MFA1P_CHICK	Microfibrillar-associated protein 1 (Associated microfibril protein) (AMF)	0.82	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				442
P78559 UniProt NPD GO	MAP1A_HUMAN	Microtubule-associated protein 1A (MAP 1A) (Proliferation-related protein p80) [Contains: MAP1 light ...	0.82	+	nuc	0		microtubule associated complex [TAS]	600178		2805
Q36665 UniProt NPD GO	RT12_PINSY	Mitochondrial ribosomal protein S12	0.82	-	nuc	0	Mitochondrion				125
Q62925 UniProt NPD GO	M3K1_RAT	Mitogen-activated protein kinase kinase kinase 1 (EC 2.7.11.25) (MAPK/ERK kinase kinase 1) (MEK kina ...	0.82	-	nuc	0	Membrane; peripheral membrane protein				1493
Q5U303 UniProt NPD GO	TAB2_RAT	Mitogen-activated protein kinase kinase kinase 7-interacting protein 2	0.82	-	nuc	0	Nucleus (By similarity). Cytoplasm; cytosol (By similarity). Cytoplasmic when activated. Following I ...				693
Q9NYJ8 UniProt NPD GO	TAB2_HUMAN	Mitogen-activated protein kinase kinase kinase 7-interacting protein 2 (TAK1-binding protein 2)	0.82	-	nuc	0	Membrane; peripheral membrane protein. Cytoplasm; cytosol. Following IL1 stimulation, translocation ...		605101		693
Q5AJS6 UniProt NPD GO	MRD1_CANAL	Multiple RNA-binding domain-containing protein 1	0.82	+	nuc	0	Nucleus (By similarity)				841
Q7YS82 UniProt NPD GO	MYOD1_BOVIN	Myoblast determination protein 1	0.82	+	nuc	0	Nucleus (By similarity)				318
P49811 UniProt NPD GO	MYOD1_PIG	Myoblast determination protein 1	0.82	+	nuc	0	Nucleus				319
P13349 UniProt NPD GO	MYF5_HUMAN	Myogenic factor 5 (Myf-5)	0.82	+	nuc	0	Nucleus		159990		255
Q6PUV5 UniProt NPD GO	MYF6_TETNG	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.82	+	nuc	0	Nucleus (By similarity)				239
P17920 UniProt NPD GO	MYOG_CHICK	Myogenin (Myogenic factor)	0.82	+	nuc	0	Nucleus				227
Q86TC9 UniProt NPD GO	MYPN_HUMAN	Myopalladin (145 kDa sarcomeric protein)	0.82	-	nuc	0	Cytoplasm. Bound to sarcomere both at the Z-line periphery and in the central I-band region. Nucleus ...		608517		1320
P39922 UniProt NPD GO	MYS3_HYDAT	Myosin heavy chain, clone 203 (Fragment)	0.82	-	nuc	0					539
Q875X4 UniProt NPD GO	MYO2B_SACCA	Myosin-2B (Class V unconventional myosin MYO2B) (Type V myosin heavy chain MYO2B) (Myosin V MYO2B)	0.82	-	nuc	0					1419
O42917 UniProt NPD GO	ESO1_SCHPO	N-acetyltransferase eso1 (EC 2.3.1.-) (Sister chromatid cohesion protein eso1) (ECO1 homolog)	0.82	-	nuc	0	Nucleus (Probable)				872
P59045 UniProt NPD GO	NAL11_HUMAN	NACHT, LRR and PYD-containing protein 11 (PYRIN-containing APAF1-like protein 6) (Nucleotide-binding ...	0.82	-	vac	0			609664		1033
Q6N069 UniProt NPD GO	NARGL_HUMAN	NMDA receptor-regulated 1-like protein (NARG1-like protein)	0.82	-	nuc	0		cytoplasm [ISS] nucleus [ISS] transcription factor complex [ISS]			864
O14513 UniProt NPD GO	NAP5_HUMAN	Nck-associated protein 5 (NAP-5) (Fragment)	0.82	-	nuc	0			608789		416
O00401 UniProt NPD GO	WASL_HUMAN	Neural Wiskott-Aldrich syndrome protein (N-WASP)	0.82	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Preferentially localized in the cytoplasm when p ...	actin cytoskeleton [TAS]	605056		505
Q60430 UniProt NPD GO	NDF1_MESAU	Neurogenic differentiation factor 1 (NeuroD1) (Beta-cell E-box trans-activator 2) (BETA2)	0.82	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				355
Q13562 UniProt NPD GO	NDF1_HUMAN	Neurogenic differentiation factor 1 (NeuroD1) (NeuroD)	0.82	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		606394		356
Q96NK8 UniProt NPD GO	NDF6_HUMAN	Neurogenic differentiation factor 6 (NeuroD6)	0.82	-	nuc	0	Nucleus (Probable)				337

You are viewing entries 7901 to 7950 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.