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
P06719 UniProt NPD GO	KNOB_PLAFN	Knob-associated histidine-rich protein precursor (KAHRP)	0.80	+	nuc	0	Host: Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of the membrane ...				657
P09346 UniProt NPD GO	KNOB_PLAFG	Knob-associated histidine-rich protein precursor (KAHRP) (KP)	0.80	+	nuc	0	Host: Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of the membrane ...				634
O00522 UniProt NPD GO	KRIT1_HUMAN	Krev interaction trapped protein 1 (Krev interaction trapped 1) (Cerebral cavernous malformations 1 ...	0.80	+	nuc	0	Membrane; peripheral membrane protein (Probable)		604214		736
O95600 UniProt NPD GO	KLF8_HUMAN	Krueppel-like factor 8 (Basic krueppel-like factor 3) (Zinc finger protein 741)	0.80	+	nuc	0	Nucleus		300286		359
Q61789 UniProt NPD GO	LAMA3_MOUSE	Laminin alpha-3 chain precursor (Nicein subunit alpha)	0.80	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [IDA]			3333
Q6UY01 UniProt NPD GO	LRC31_HUMAN	Leucine-rich repeat-containing protein 31	0.80	-	nuc	0					552
Q8K1C9 UniProt NPD GO	LRC41_MOUSE	Leucine-rich repeat-containing protein 41 (Protein Muf1)	0.80	-	nuc	0					785
Q922Q8 UniProt NPD GO	LRC59_MOUSE	Leucine-rich repeat-containing protein 59	0.80	+	nuc	1	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				307
Q9XJ60 UniProt NPD GO	MAD50_ORYSA	MADS-box transcription factor 50 (OsMADS50) (Protein SUPPRESSOR OF CONSTANS OVEREXPRESSION 1-like) ( ...	0.80	-	nuc	0	Nucleus (Probable)				230
Q6P7N1 UniProt NPD GO	RBM13_XENTR	MAK16-like protein RBM13 (RNA-binding motif protein 13-like)	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				300
Q7ZYG5 UniProt NPD GO	R13LB_XENLA	MAK16-like protein RBM13 B (RNA-binding motif protein 13-like B)	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				304
P53599 UniProt NPD GO	SSK2_YEAST	MAP kinase kinase kinase SSK2 (EC 2.7.11.25) (Suppressor of sensor kinase 2)	0.80	-	nuc	0		bud neck [IDA] bud tip [IDA] cytosol [IDA]			1579
Q66I46 UniProt NPD GO	MKNK2_XENTR	MAP kinase-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.80	-	nuc	0					466
Q9FI00 UniProt NPD GO	MLO11_ARATH	MLO-like protein 11 (AtMlo11)	0.80	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				573
Q9P445 UniProt NPD GO	MAT2_COCSA	Mating-type protein MAT-2	0.80	-	nuc	0	Nucleus (Potential)				337
Q8WJR5 UniProt NPD GO	MATK_ADEFA	Maturase K (Intron maturase)	0.80	-	cyt	0	Plastid; chloroplast				504
Q9GF37 UniProt NPD GO	MATK_ARAKO	Maturase K (Intron maturase)	0.80	-	nuc	0	Plastid; chloroplast				504
Q6LA04 UniProt NPD GO	MATK_JUNEF	Maturase K (Intron maturase)	0.80	+	cyt	0	Plastid; chloroplast				517
Q8M998 UniProt NPD GO	MATK_OLEEU	Maturase K (Intron maturase)	0.80	-	nuc	0	Plastid; chloroplast				506
Q9GF47 UniProt NPD GO	MATK_OLIPU	Maturase K (Intron maturase)	0.80	-	nuc	0	Plastid; chloroplast				504
Q507R6 UniProt NPD GO	MATK_RANAC	Maturase K (Intron maturase)	0.80	-	cyt	0	Plastid; chloroplast				507
Q507Q9 UniProt NPD GO	MATK_RANLI	Maturase K (Intron maturase)	0.80	-	cyt	0	Plastid; chloroplast				508
Q9MUX3 UniProt NPD GO	MATK_SORBI	Maturase K (Intron maturase)	0.80	-	cyt	0	Plastid; chloroplast				515
P26859 UniProt NPD GO	RM02_MARPO	Mitochondrial 60S ribosomal protein L2	0.80	-	mit	0	Mitochondrion				501
Q8BPM2 UniProt NPD GO	M4K5_MOUSE	Mitogen-activated protein kinase kinase kinase kinase 5 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.80	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			847
Q86B87 UniProt NPD GO	MMD4_DROME	Modifier of mdg4	0.80	-	nuc	0	Nucleus. Colocalizes with other elements of the gypsy chromatin insulator complex at multiple sites ...	chromatin [IMP] nucleus [IDA] polytene chromosome [IDA]			610
P22711 UniProt NPD GO	TIN_DROME	Muscle-specific homeobox protein tinman (Msh-2) (NK-4)	0.80	+	nuc	0	Nucleus (Probable)				416
P34219 UniProt NPD GO	YBF4_YEAST	Myb domain-containing protein YBL054W	0.80	-	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			525
Q08759 UniProt NPD GO	MYB_XENLA	Myb protein	0.80	+	nuc	0	Nucleus				624
P46200 UniProt NPD GO	MYB_BOVIN	Myb proto-oncogene protein (C-myb)	0.80	+	nuc	0	Nucleus				640
Q8CFN5 UniProt NPD GO	MEF2C_MOUSE	Myocyte-specific enhancer factor 2C	0.80	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			474
P47807 UniProt NPD GO	MYO1A_CHICK	Myosin Ia (Brush border myosin I) (BBM-I) (BBMI) (Myosin I heavy chain) (MIHC)	0.80	-	cyt	0				1AJI	1045
Q63356 UniProt NPD GO	MYO1E_RAT	Myosin Ie (Myosin heavy chain myr 3)	0.80	-	nuc	0					1107
P19524 UniProt NPD GO	MYO2_YEAST	Myosin-2 (Class V unconventional myosin MYO2) (Type V myosin heavy chain MYO2) (Myosin V MYO2) (Cell ...	0.80	-	cyt	0	Concentrates to sites of polarized growth, namely to the bud tip during S and G2 phases of the cell ...	actin cable [IDA] actin cap [IDA]		2F6H	1574
P59047 UniProt NPD GO	NALP5_HUMAN	NACHT, LRR and PYD-containing protein 5 (Mater protein homolog)	0.80	-	nuc	0			609658		1200
Q8BKJ9 UniProt NPD GO	SIRT7_MOUSE	NAD-dependent deacetylase sirtuin-7 (EC 3.5.1.-) (SIR2-like protein 7)	0.80	-	nuc	0	Cytoplasm. Located under the nuclear membrane (By similarity)				402
Q9Y5A7 UniProt NPD GO	NUB1_HUMAN	NEDD8 ultimate buster 1 (NY-REN-18 antigen)	0.80	+	nuc	0	Nucleus. Predominantly		607981	1WJU	615
Q9WUU8 UniProt NPD GO	NAF1_MOUSE	Nef-associated factor 1 (Naf1) (TNFAIP3-interacting protein 1) (A20-binding inhibitor of NF-kappa-B ...	0.80	-	nuc	0	Cytoplasm	cytoplasm [IDA]			647
Q15025 UniProt NPD GO	NAF1_HUMAN	Nef-associated factor 1 (Naf1) (TNFAIP3-interacting protein 1) (HIV-1 Nef-interacting protein) (Viri ...	0.80	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and cytoplasm in a CRM1-dependent manner	intracellular [TAS]	607714		636
P07207 UniProt NPD GO	NOTCH_DROME	Neurogenic locus Notch protein precursor	0.80	-	exc	1 *	Cell membrane; single-pass type I membrane protein. Processed form: Nucleus. Upon activation and S3 ...	integral to membrane [TAS] intracellular [IDA] nucleus [TAS] plasma membrane [IDA]		1OT8	2703
O35516 UniProt NPD GO	NOTC2_MOUSE	Neurogenic locus notch homolog protein 2 precursor (Notch 2) (Motch B) [Contains: Notch 2 extracellu ...	0.80	-	exc	2	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	cell surface [ISS] integral to plasma membrane [IC] nucleus [IDA]			2470
Q9QW30 UniProt NPD GO	NOTC2_RAT	Neurogenic locus notch homolog protein 2 precursor (Notch 2) [Contains: Notch 2 extracellular trunca ...	0.80	-	exc	2	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	cell surface [ISS] integral to plasma membrane [ISS] nucleus [ISS]			2471
P20783 UniProt NPD GO	NT3_HUMAN	Neurotrophin-3 precursor (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2)	0.80	-	nuc	0	Secreted protein		162660	1NT3	257
Q501R9 UniProt NPD GO	NBR1_RAT	Next to BRCA1 gene 1 protein (Neighbor of BRCA1 gene 1 protein)	0.80	-	nuc	0	In cardiac muscles localizes to the sarcomeric M band				983
Q06178 UniProt NPD GO	NMA1_YEAST	Nicotinamide-nucleotide adenylyltransferase 1 (EC 2.7.7.1) (NAD(+) pyrophosphorylase 1) (NAD(+) diph ...	0.80	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			401
Q21006 UniProt NPD GO	NHR34_CAEEL	Nuclear hormone receptor family member nhr-34	0.80	-	nuc	0	Nucleus (Potential)				605
Q13352 UniProt NPD GO	NRIF3_HUMAN	Nuclear receptor-interacting factor 3 (Integrin beta-3-binding protein) (Beta3-endonexin)	0.80	-	nuc	0	Isoform 1, isoform 2, isoform 3: Nucleus. Isoform 3, isoform 4: Cytoplasm. Isoform 3 is predominantl ...	cytoplasm [TAS] membrane fraction [TAS] nucleus [TAS]	605494		177
Q9CQ82 UniProt NPD GO	NRIF3_MOUSE	Nuclear receptor-interacting factor 3 (Integrin beta-3-binding protein) (Beta3-endonexin)	0.80	-	nuc	0	Nucleus (By similarity)				176
Q6FWS1 UniProt NPD GO	NOG2_CANGA	Nucleolar GTP-binding protein 2	0.80	-	nuc	0	Nucleus; nucleolus (By similarity)				494
Q6CKV6 UniProt NPD GO	NOP12_KLULA	Nucleolar protein 12	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				524

You are viewing entries 8951 to 9000 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.