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
P70615 UniProt NPD GO	LMNB1_RAT	Lamin-B1	0.89	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side (By similarity)				586
P14732 UniProt NPD GO	LMNB2_CHICK	Lamin-B2	0.89	+	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side				600
Q03427 UniProt NPD GO	LAMC_DROME	Lamin-C (pG-IF)	0.89	-	mit	0	Nucleus. Nuclear periphery	lamin filament [NAS]			621
Q86V48 UniProt NPD GO	LUZP1_HUMAN	Leucine zipper protein 1	0.89	-	nuc	0	Nucleus. Also detected in soma and dendrites of neurons (By similarity)		601422		1076
Q8CFC9 UniProt NPD GO	LZTS1_RAT	Leucine zipper putative tumor suppressor 1 (PSD-Zip70)	0.89	-	nuc	0	Cytoplasm. Cell membrane (By similarity). Associated with the plasma membrane and with microtubules ...				600
Q4R3F0 UniProt NPD GO	LRRC6_MACFA	Leucine-rich repeat-containing protein 6	0.89	-	nuc	0	Cytoplasm (By similarity)				466
O75334 UniProt NPD GO	LIPA2_HUMAN	Liprin-alpha-2 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 ...	0.89	-	nuc	0	Cytoplasm. Cell surface. Colocalizes with PTPRF at the cell surface	cytoplasm [TAS]	603143		1257
Q8BSS9 UniProt NPD GO	LIPA2_MOUSE	Liprin-alpha-2 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 ...	0.89	-	nuc	0	Cytoplasm (By similarity). Cell surface (By similarity). Colocalizes with PTPRF at the cell surface ...	synaptosome [IDA]			1257
O75335 UniProt NPD GO	LIPA4_HUMAN	Liprin-alpha-4 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-4 ...	0.89	-	nuc	0	Cytoplasm (By similarity). Cell surface (By similarity). Colocalizes with PTPRF at the cell surface ...	intracellular [TAS]	603145		701
P28584 UniProt NPD GO	TRK2_YEAST	Low-affinity potassium transport protein	0.89	+	end	10 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			889
Q9UJU2 UniProt NPD GO	LEF1_HUMAN	Lymphoid enhancer-binding factor 1 (LEF-1) (T cell-specific transcription factor 1-alpha) (TCF1-alph ...	0.89	+	nuc	0	Nucleus (By similarity). Found in nuclear bodies upon PIASG binding (By similarity)		153245		399
Q8K4J6 UniProt NPD GO	MKL1_MOUSE	MKL/myocardin-like protein 1 (Myocardin-related transcription factor A) (MRTF-A) (Megakaryoblastic l ...	0.89	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			964
P59759 UniProt NPD GO	MKL2_MOUSE	MKL/myocardin-like protein 2 (Myocardin-related transcription factor B) (MRTF-B)	0.89	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IC]			1080
Q707Y8 UniProt NPD GO	MTAL2_PICAN	Mating-type protein ALPHA2 (MATalpha2 transcription factor)	0.89	-	nuc	0	Nucleus (By similarity)				163
O35618 UniProt NPD GO	MDM4_MOUSE	Mdm4 protein (p53-binding protein Mdm4) (Mdm2-like p53-binding protein) (Mdmx protein) (Double minut ...	0.89	-	nuc	0	Nucleus	nucleus [ISS]			489
O13606 UniProt NPD GO	MEI4_SCHPO	Meiosis-specific transcription factor mei4	0.89	-	nuc	0	Nucleus (Probable)				517
Q6FX33 UniProt NPD GO	MSC3_CANGA	Meiotic sister-chromatid recombination protein 3	0.89	+	nuc	0	Cell membrane; peripheral membrane protein. Cell periphery (By similarity)				834
O88382 UniProt NPD GO	MAGI2_RAT	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (Membrane-associated gu ...	0.89	+	nuc	0	Synaptosome; peripheral membrane protein. Membrane-associated in synaptosomes				1277
P0C090 UniProt NPD GO	MNAB_MOUSE	Membrane-associated nucleic acid-binding protein	0.89	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Intracytoplasmic membrane (By similarity). Membrane-a ...				1187
Q13330 UniProt NPD GO	MTA1_HUMAN	Metastasis-associated protein MTA1	0.89	+	nuc	0	Isoform Short: Cytoplasm. Isoform Long: Nucleus		603526		715
O95243 UniProt NPD GO	MBD4_HUMAN	Methyl-CpG-binding domain protein 4 (EC 3.2.2.-) (Methyl-CpG-binding protein MBD4) (Methyl-CpG-bindi ...	0.89	-	nuc	0	Nucleus	nucleus [TAS]	603574		580
P51608 UniProt NPD GO	MECP2_HUMAN	Methyl-CpG-binding protein 2 (MeCP-2 protein) (MeCP2)	0.89	+	nuc	0	Nucleus. Colocalized with methyl-CpG in the genome	nucleus [TAS]	105830	1QK9	486
Q95LG8 UniProt NPD GO	MECP2_MACFA	Methyl-CpG-binding protein 2 (MeCP-2 protein) (MeCP2)	0.89	+	nuc	0	Nucleus (By similarity). Colocalized with methyl-CpG in the genome (By similarity)				486
Q9Z2D6 UniProt NPD GO	MECP2_MOUSE	Methyl-CpG-binding protein 2 (MeCP-2 protein) (MeCP2)	0.89	+	nuc	0	Nucleus. Colocalized with methyl-CpG in the genome	cytosol [IDA] heterochromatin [IDA] nucleus [IDA]			484
O75030 UniProt NPD GO	MITF_HUMAN	Microphthalmia-associated transcription factor	0.89	+	nuc	0	Nucleus	nucleus [NAS]	193510		526
Q12482 UniProt NPD GO	AGC1_YEAST	Mitochondrial aspartate-glutamate transporter AGC1 (Aspartate-glutamate carrier 1)	0.89	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				902
Q13233 UniProt NPD GO	M3K1_HUMAN	Mitogen-activated protein kinase kinase kinase 1 (EC 2.7.11.25) (MAPK/ERK kinase kinase 1) (MEK kina ...	0.89	-	nuc	0			600982		1495
Q9Y2U5 UniProt NPD GO	M3K2_HUMAN	Mitogen-activated protein kinase kinase kinase 2 (EC 2.7.11.25) (MAPK/ERK kinase kinase 2) (MEK kina ...	0.89	-	nuc	0	Cytoplasm. Upon EGF stimulation, translocates into the nucleus		609487	2CU1	619
Q24564 UniProt NPD GO	MERH_DROME	Moesin/ezrin/radixin homolog 2 (Ezrin-moesin-radixin 2) (Merlin) (dMerlin)	0.89	-	nuc	0	Cell membrane; cell-cell junction; adherens junction; peripheral membrane protein. Intracellular mem ...	adherens junction [IDA] apical plasma membrane [TAS] cytoplasm [IDA] plasma membrane [IDA] zonula adherens [TAS]			635
Q9ERZ3 UniProt NPD GO	ACM3_MOUSE	Muscarinic acetylcholine receptor M3 (Mm3 mAChR)	0.89	+	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			589
Q92020 UniProt NPD GO	MYF6_XENLA	Myogenic factor 6 (Myf-6) (Muscle-specific regulatory factor 4)	0.89	+	nuc	0	Nucleus (By similarity)				240
P22816 UniProt NPD GO	MYOD_DROME	Myogenic-determination protein (Protein nautilus) (dMyd)	0.89	+	nuc	0	Nucleus	nucleus [TAS]			332
Q9JLT0 UniProt NPD GO	MYH10_RAT	Myosin-10 (Myosin heavy chain, nonmuscle IIb) (Nonmuscle myosin heavy chain IIb) (NMMHC II-b) (NMMHC ...	0.89	+	nuc	0					1976
Q7Z406 UniProt NPD GO	MYH14_HUMAN	Myosin-14 (Myosin heavy chain, nonmuscle IIc) (Nonmuscle myosin heavy chain IIc) (NMHC II-C)	0.89	+	nuc	0			608568		1995
P35579 UniProt NPD GO	MYH9_HUMAN	Myosin-9 (Myosin heavy chain, nonmuscle IIa) (Nonmuscle myosin heavy chain IIa) (NMMHC II-a) (NMMHC- ...	0.89	+	nuc	0			605249		1959
Q3T906 UniProt NPD GO	GNPTA_HUMAN	N-acetylglucosamine-1-phosphotransferase subunits alpha/beta precursor (EC 2.7.8.17) (GlcNAc-1-phosp ...	0.89	-	mit	2 *	Subunit alpha: Golgi apparatus; Golgi membrane; single-pass type I membrane protein. Subunit beta: G ...		607840		1256
P12945 UniProt NPD GO	NAT1_YEAST	N-terminal acetyltransferase A complex subunit NAT1 (NatA complex subunit NAT1) (Amino-terminal, alp ...	0.89	-	nuc	0	Cytoplasm	mitochondrion [IDA] NatA complex [IDA]			853
Q96EB6 UniProt NPD GO	SIRT1_HUMAN	NAD-dependent deacetylase sirtuin-1 (EC 3.5.1.-) (hSIRT1) (hSIR2) (SIR2-like protein 1)	0.89	+	nuc	0	Nucleus. Recruited to the nuclear bodies via its interaction with PML		604479		747
Q8BY02 UniProt NPD GO	NKRF_MOUSE	NF-kappa-B-repressing factor (NFKB-repressing factor) (Transcription factor NRF)	0.89	+	nuc	0	Nucleus; nucleolus (By similarity)				690
P19426 UniProt NPD GO	NELFE_MOUSE	Negative elongation factor E (NELF-E) (RD protein)	0.89	+	nuc	0	Nucleus				375
O08816 UniProt NPD GO	WASL_RAT	Neural Wiskott-Aldrich syndrome protein (N-WASP)	0.89	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Preferentially localized in the cytoplasm when p ...			1MKE	501
P97526 UniProt NPD GO	NF1_RAT	Neurofibromin (Neurofibromatosis-related protein NF-1)	0.89	-	mit	0					2820
P21359 UniProt NPD GO	NF1_HUMAN	Neurofibromin (Neurofibromatosis-related protein NF-1) [Contains: Neurofibromin truncated]	0.89	-	mit	0		cytoplasm [TAS]	162200	2D4Q	2839
Q99743 UniProt NPD GO	NPAS2_HUMAN	Neuronal PAS domain-containing protein 2 (Neuronal PAS2) (Member of PAS protein 4) (MOP4)	0.89	+	nuc	0	Nucleus (Potential)		603347		824
Q8N4C6 UniProt NPD GO	NIN_HUMAN	Ninein (hNinein)	0.89	+	nuc	0	Centrosome. Component of the core centrosome. Arranged in a tubular conformation with an open and a ...	centrosome [IDA]	608684		2090
P23503 UniProt NPD GO	NAR1_YEAST	Nuclear architecture-related protein 1	0.89	-	nuc	0		cytosol [IDA] membrane [IDA]			491
Q14938 UniProt NPD GO	NFIX_HUMAN	Nuclear factor 1 X-type (Nuclear factor 1/X) (NF1-X) (NFI-X) (NF-I/X) (CCAAT-box-binding transcripti ...	0.89	-	nuc	0	Nucleus		164005		502
P13623 UniProt NPD GO	NFIX_MESAU	Nuclear factor 1 X-type (Nuclear factor 1/X) (NF1-X) (NFI-X) (NF-I/X) (CCAAT-box-binding transcripti ...	0.89	-	nuc	0	Nucleus				441
Q60591 UniProt NPD GO	NFAC2_MOUSE	Nuclear factor of activated T-cells, cytoplasmic 2 (T cell transcription factor NFAT1) (NFAT pre-exi ...	0.89	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...	cytoplasm [IDA]			1064
Q6P4R8 UniProt NPD GO	NFRKB_HUMAN	Nuclear factor related to kappa-B-binding protein (DNA-binding protein R kappa-B)	0.89	+	nuc	0	Nucleus (Probable)		164013		1299

You are viewing entries 4701 to 4750 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.