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
Q6BDH0 UniProt NPD GO	MATK_PINTB	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
Q00866 UniProt NPD GO	MATK_PINTH	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				515
O78252 UniProt NPD GO	MATK_ROSCA	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
O78248 UniProt NPD GO	MATK_ROSFO	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
Q9BCJ9 UniProt NPD GO	MATK_ROSMU	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				503
Q589A9 UniProt NPD GO	MATK_SILLA	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				503
Q9M3N0 UniProt NPD GO	MATK_SPIOL	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				505
Q52TG6 UniProt NPD GO	MATK_TYPAN	Maturase K (Intron maturase)	0.75	-	nuc	0	Plastid; chloroplast				513
Q8WJN0 UniProt NPD GO	MATK_VAUCA	Maturase K (Intron maturase)	0.75	-	cyt	0	Plastid; chloroplast				504
Q09739 UniProt NPD GO	MCP7_SCHPO	Meiotic coiled-coil protein 7	0.75	+	nuc	0		nuclear chromatin [IDA]			210
Q08550 UniProt NPD GO	MPC54_YEAST	Meiotic plaque component protein 54	0.75	-	nuc	0	Localizes to prospore membrane. Localizes to the ends of spindle microtubules in cells in meiosis. L ...	spindle pole body [IDA]			464
Q9Z2A6 UniProt NPD GO	MK15_RAT	Mitogen-activated protein kinase 15 (EC 2.7.11.24) (Extracellular signal-regulated kinase 7)	0.75	-	nuc	0	Nucleus	extracellular region [ISS] intracellular [ISS] nucleus [IDA]			547
Q9Z1S0 UniProt NPD GO	BUB1B_MOUSE	Mitotic checkpoint serine/threonine-protein kinase BUB1 beta (EC 2.7.11.1) (MAD3/BUB1-related protei ...	0.75	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in interphase cells. Bound to BUB3 o ...	kinetochore [IDA] outer kinetochore of condensed chromosome [IDA]			1052
Q10277 UniProt NPD GO	MSA1_SCHPO	Multicopy suppressor of sporulation protein msa1	0.75	+	nuc	0	Cytoplasm				533
O60682 UniProt NPD GO	MUSC_HUMAN	Musculin (Activated B-cell factor 1) (ABF-1)	0.75	-	nuc	0	Nucleus	nucleus [TAS]	603628		206
Q27966 UniProt NPD GO	MYO1C_BOVIN	Myosin Ic (Myosin I beta) (MMI-beta) (MMIb)	0.75	-	cyt	0					1028
Q35322 UniProt NPD GO	NUGM_ORYSA	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.75	-	nuc	0	Mitochondrion; mitochondrial inner membrane				190
Q13506 UniProt NPD GO	NAB1_HUMAN	NGFI-A-binding protein 1 (EGR-1-binding protein 1) (Transcriptional regulatory protein p54)	0.75	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	600800		487
Q63689 UniProt NPD GO	NDF2_RAT	Neurogenic differentiation factor 2 (NeuroD2) (Brain bHLH protein KW8)	0.75	+	nuc	0	Nucleus (Probable)				382
Q95150 UniProt NPD GO	NT3_CEREL	Neurotrophin-3 precursor (NT-3) (Fragment)	0.75	-	nuc	0	Secreted protein				154
P25433 UniProt NPD GO	NT3_CHICK	Neurotrophin-3 precursor (NT-3) (Neurotrophic factor) (HDNF) (Nerve growth factor 2) (NGF-2)	0.75	-	exc	0	Secreted protein				257
O61309 UniProt NPD GO	NOS_LYMST	Nitric-oxide synthase (EC 1.14.13.39) (NOS type I) (Neuronal NOS) (N-NOS) (nNOS)	0.75	-	nuc	0					1153
Q6DIE2 UniProt NPD GO	NCBP1_XENTR	Nuclear cap-binding protein subunit 1	0.75	+	mit	0	Nucleus (By similarity)	nucleus [ISS]			791
Q6GQ80 UniProt NPD GO	NBP1A_XENLA	Nuclear cap-binding protein subunit 1-A	0.75	+	mit	0	Nucleus (By similarity)				791
Q91431 UniProt NPD GO	NF7O_XENLA	Nuclear factor 7, ovary (xNF7-O)	0.75	-	nuc	0	Nucleus (By similarity)				610
Q8BJ71 UniProt NPD GO	NUP93_MOUSE	Nuclear pore complex protein Nup93 (Nucleoporin Nup93) (93 kDa nucleoporin) (CBP-interacting protein ...	0.75	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Localizes at the nuclear basket and ...				819
Q02819 UniProt NPD GO	NUCB1_MOUSE	Nucleobindin-1 precursor (CALNUC)	0.75	-	exc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripheral membrane protein; luminal ...				459
Q63083 UniProt NPD GO	NUCB1_RAT	Nucleobindin-1 precursor (CALNUC) (Bone 63 kDa calcium-binding protein)	0.75	-	exc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripheral membrane protein; luminal ...				459
Q9NR30 UniProt NPD GO	DDX21_HUMAN	Nucleolar RNA helicase 2 (EC 3.6.1.-) (Nucleolar RNA helicase II) (Nucleolar RNA helicase Gu) (RH II ...	0.75	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]	606357		783
Q9JIK5 UniProt NPD GO	DDX21_MOUSE	Nucleolar RNA helicase 2 (EC 3.6.1.-) (Nucleolar RNA helicase II) (Nucleolar RNA helicase Gu) (RH II ...	0.75	+	nuc	0	Nucleus; nucleolus				851
Q5AHI7 UniProt NPD GO	NOP12_CANAL	Nucleolar protein 12	0.75	+	nuc	0	Nucleus; nucleolus (By similarity)				454
P40991 UniProt NPD GO	NOP2_YEAST	Nucleolar protein 2	0.75	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			618
Q8R322 UniProt NPD GO	GLE1_MOUSE	Nucleoporin GLE1 (GLE1-like protein)	0.75	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm. ...				699
P35729 UniProt NPD GO	NU120_YEAST	Nucleoporin NUP120 (Nuclear pore protein NUP120)	0.75	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			1037
Q8N6M0 UniProt NPD GO	OTU6B_HUMAN	OTU domain-containing protein 6B	0.75	+	nuc	0					293
P39720 UniProt NPD GO	OAF1_YEAST	Oleate-activated transcription factor 1	0.75	-	end	0	Nucleus	nucleus [IPI]			1047
Q7YS99 UniProt NPD GO	OPTN_PIG	Optineurin	0.75	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus (By similarity). Found in the perinuc ...				574
P22829 UniProt NPD GO	NR4A1_RAT	Orphan nuclear receptor NR4A1 (Orphan nuclear receptor HMR) (Nerve growth factor-induced protein I-B ...	0.75	-	nuc	0	Nucleus			1YJE	597
O74755 UniProt NPD GO	PST3_SCHPO	Paired amphipathic helix protein pst3 (SIN3 homolog 3)	0.75	-	nuc	0	Nucleus (By similarity)				1154
O73917 UniProt NPD GO	PAX6_ORYLA	Paired box protein Pax-6	0.75	+	nuc	0	Nucleus				437
Q967Z0 UniProt NPD GO	MYSP_DERFA	Paramyosin (Allergen Der f 11) (Antigen Df642) (Fragment)	0.75	-	nuc	0	Thick filaments of the myofibrils				692
O02811 UniProt NPD GO	PI4KA_BOVIN	Phosphatidylinositol 4-kinase alpha (EC 2.7.1.67) (PI4-kinase alpha) (PtdIns-4-kinase alpha) (PI4K-a ...	0.75	-	cyt	0					2043
O14986 UniProt NPD GO	PI51B_HUMAN	Phosphatidylinositol-4-phosphate 5-kinase type-1 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.75	-	nuc	0	Intracytoplasmic membrane (By similarity). Associated with membranes (By similarity)		602745		540
Q5R9I3 UniProt NPD GO	PI3R4_PONPY	Phosphoinositide 3-kinase regulatory subunit 4 (EC 2.7.11.1) (PI3-kinase regulatory subunit 4)	0.75	-	nuc	0					1357
Q9WV78 UniProt NPD GO	PLVAP_RAT	Plasmalemma vesicle-associated protein (Plasmalemma vesicle protein 1) (PV-1) (gp68)	0.75	-	nuc	1 *	Cell membrane; single-pass type II membrane protein. Membrane-associated protein of caveolae. Found ...	caveola [IDA] integral to membrane [IDA]			438
P30067 UniProt NPD GO	RK20_EPIVI	Plastid 50S ribosomal protein L20	0.75	-	mit	0	Plastid				127
Q8BUL6 UniProt NPD GO	PKHA1_MOUSE	Pleckstrin homology domain-containing family A member 1 (Tandem PH domain-containing protein 1) (TAP ...	0.75	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Nucleus (By s ...				383
P60669 UniProt NPD GO	PKHA4_RAT	Pleckstrin homology domain-containing family A member 4 (Phosphoinositol 3-phosphate-binding protein ...	0.75	+	mit	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Probable)				779
O88705 UniProt NPD GO	HCN3_MOUSE	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (Hyperpolarization-ac ...	0.75	-	end	1	Membrane; multi-pass membrane protein				779
O70507 UniProt NPD GO	HCN4_MOUSE	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 (Brain cyclic nucleot ...	0.75	-	nuc	2	Membrane; multi-pass membrane protein				1186

You are viewing entries 11451 to 11500 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.