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
Q9ESV1 UniProt NPD GO	LUZP1_RAT	Leucine zipper protein 1 (Leucine zipper motif-containing protein)	0.92	-	nuc	0	Nucleus. Also detected in soma and dendrites of neurons				1051
Q5S007 UniProt NPD GO	LRRK2_HUMAN	Leucine-rich repeat serine/threonine-protein kinase 2 (EC 2.7.11.1) (Dardarin)	0.92	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Localized in the cytoplasm and associated with cel ...		609007		2527
Q80XG9 UniProt NPD GO	LRTM4_MOUSE	Leucine-rich repeat transmembrane neuronal protein 4 precursor	0.92	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				590
P06800 UniProt NPD GO	CD45_MOUSE	Leukocyte common antigen precursor (EC 3.1.3.48) (L-CA) (Lymphocyte common antigen Ly-5) (CD45 antig ...	0.92	-	exc	2	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] focal adhesion [IDA] integral to plasma membrane [ISS]			1291
P04157 UniProt NPD GO	CD45_RAT	Leukocyte common antigen variant 4 precursor (EC 3.1.3.48) (L-CA) (CD45 antigen) (T200) (Fragment)	0.92	-	nuc	2	Membrane; single-pass type I membrane protein	focal adhesion [ISS] integral to plasma membrane [IDA] internal side of plasma membrane [TAS]			1255
Q8C8U0 UniProt NPD GO	LIPB1_MOUSE	Liprin-beta-1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding ...	0.92	-	nuc	0					969
Q09101 UniProt NPD GO	HIG_DROME	Locomotion-related protein Hikaru genki precursor	0.92	-	nuc	0	Secreted protein				958
Q29029 UniProt NPD GO	MPIP3_PIG	M-phase inducer phosphatase 3 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25C)	0.92	+	nuc	0	Nucleus				502
Q99549 UniProt NPD GO	MPP8_HUMAN	M-phase phosphoprotein 8	0.92	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			860
P79621 UniProt NPD GO	C2TA_MOUSE	MHC class II transactivator (CIITA)	0.92	-	nuc	0	Nucleus	nucleus [IC]			1155
Q8IY33 UniProt NPD GO	MILK2_HUMAN	MICAL-like protein 2	0.92	-	nuc	0	Cytoplasm (By similarity)				904
Q8K310 UniProt NPD GO	MATR3_MOUSE	Matrin-3	0.92	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)			1X4F	846
Q5U2M8 UniProt NPD GO	MDC1_RAT	Mediator of DNA damage checkpoint protein 1	0.92	-	nuc	0	Nucleus (By similarity). Associated with chromatin. Relocalizes to discrete nuclear foci following D ...				1279
Q74ZL3 UniProt NPD GO	MSC3_ASHGO	Meiotic sister-chromatid recombination protein 3	0.92	-	nuc	0	Cell membrane; peripheral membrane protein. Cell periphery (By similarity)				751
Q08874 UniProt NPD GO	MITF_MOUSE	Microphthalmia-associated transcription factor	0.92	+	nuc	0	Nucleus	nucleus [IDA]			526
Q96PK2 UniProt NPD GO	MACF4_HUMAN	Microtubule-actin crosslinking factor 1, isoform 4	0.92	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] cytoskeleton [ISS]	608271		5938
Q9W596 UniProt NPD GO	FUTSC_DROME	Microtubule-associated protein futsch	0.92	+	nuc	0	Cytoplasm. Microtubule-associated	microtubule associated complex [IDA]			5412
Q9WVS8 UniProt NPD GO	MK07_MOUSE	Mitogen-activated protein kinase 7 (EC 2.7.11.24) (Extracellular signal-regulated kinase 5) (ERK-5) ...	0.92	+	nuc	0					806
Q13164 UniProt NPD GO	MK07_HUMAN	Mitogen-activated protein kinase 7 (EC 2.7.11.24) (Extracellular signal-regulated kinase 5) (ERK-5) ...	0.92	+	nuc	0			602521		815
O43318 UniProt NPD GO	M3K7_HUMAN	Mitogen-activated protein kinase kinase kinase 7 (EC 2.7.11.25) (Transforming growth factor-beta-act ...	0.92	-	nuc	0			602614	2EVA	606
Q62073 UniProt NPD GO	M3K7_MOUSE	Mitogen-activated protein kinase kinase kinase 7 (EC 2.7.11.25) (Transforming growth factor-beta-act ...	0.92	-	exc	0					579
Q8N3F8 UniProt NPD GO	MILK1_HUMAN	Molecule interacting with Rab13 (MIRab13) (MICAL-like protein 1)	0.92	-	nuc	0	Cytoplasm (By similarity)				863
P49709 UniProt NPD GO	MYC_CARAU	Myc protein (c-myc)	0.92	+	nuc	0	Nucleus				399
P52160 UniProt NPD GO	MYC_BRARE	Myc protein (c-myc) (zc-Myc)	0.92	+	nuc	0	Nucleus	nucleus [ISS]			408
Q9W4S7 UniProt NPD GO	MYC_DROME	Myc protein (dMyc1) (dMyc) (Diminutive protein)	0.92	+	nuc	0	Nucleus				717
Q8IZQ8 UniProt NPD GO	MYCD_HUMAN	Myocardin	0.92	-	nuc	0	Nucleus (By similarity)		606127		938
P13533 UniProt NPD GO	MYH6_HUMAN	Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha)	0.92	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [TAS]	160710		1939
P02563 UniProt NPD GO	MYH6_RAT	Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha)	0.92	+	nuc	0	Thick filaments of the myofibrils				1938
P79293 UniProt NPD GO	MYH7_PIG	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta)	0.92	+	nuc	0	Thick filaments of the myofibrils				1935
P02567 UniProt NPD GO	MYO1_CAEEL	Myosin-1 (Myosin heavy chain D) (MHC D) (Lethal protein 75)	0.92	-	nuc	0	Thick filaments of the myofibrils				1938
Q27991 UniProt NPD GO	MYH10_BOVIN	Myosin-10 (Myosin heavy chain, nonmuscle IIb) (Nonmuscle myosin heavy chain IIb) (NMMHC II-b) (NMMHC ...	0.92	+	nuc	0					1976
Q6URW6 UniProt NPD GO	MYH14_MOUSE	Myosin-14 (Myosin heavy chain, nonmuscle IIc) (Nonmuscle myosin heavy chain IIc) (NMHC II-C)	0.92	+	nuc	0		myosin [IDA]			2000
P05659 UniProt NPD GO	MYSN_ACACA	Myosin-2 heavy chain, non muscle (Myosin II heavy chain, non muscle)	0.92	-	nuc	0					1509
Q86UW6 UniProt NPD GO	N4BP2_HUMAN	NEDD4-binding protein 2 (EC 3.-.-.-) (N4BP2) (BCL-3-binding protein)	0.92	+	nuc	0	Cytoplasm (By similarity)				1770
Q8R151 UniProt NPD GO	ZNFX1_MOUSE	NFX1-type zinc finger-containing protein 1	0.92	+	nuc	0					1909
Q9H3P2 UniProt NPD GO	NELFA_HUMAN	Negative elongation factor A (NELF-A) (Wolf-Hirschhorn syndrome candidate 2 protein)	0.92	+	nuc	0	Nucleus		606026		549
P24686 UniProt NPD GO	BIME_EMENI	Negative regulator of mitosis	0.92	+	nuc	0					2073
O13415 UniProt NPD GO	AREA_ASPOR	Nitrogen regulatory protein areA	0.92	+	nuc	0	Nucleus				866
P48412 UniProt NPD GO	UPF3_YEAST	Nonsense-mediated mRNA decay protein 3 (Up-frameshift suppressor 3)	0.92	+	nuc	0	Nucleus	cytoplasm [TAS] nucleus [IDA] polysome [IDA]			387
Q4X1V0 UniProt NPD GO	NDE1_ASPFU	Nuclear distribution protein nudE homolog 1	0.92	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules (By similarity)				621
Q4I877 UniProt NPD GO	NDE1_GIBZE	Nuclear distribution protein nudE homolog 1	0.92	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules (By similarity)				583
O00712 UniProt NPD GO	NFIB_HUMAN	Nuclear factor 1 B-type (Nuclear factor 1/B) (NF1-B) (NFI-B) (NF-I/B) (CCAAT-box-binding transcripti ...	0.92	-	nuc	0	Nucleus	nucleus [TAS]	600728		420
Q94527 UniProt NPD GO	NFKB1_DROME	Nuclear factor NF-kappa-B p110 subunit (Relish protein) (Rel-p110) [Contains: Nuclear factor NF-kapp ...	0.92	+	nuc	0	Nuclear factor NF-kappa-B p68 subunit: Nucleus. Nuclear factor NF-kappa-B p110 subunit, Nuclear fact ...	cytoplasm [IDA] nucleus [IDA]			971
O94916 UniProt NPD GO	NFAT5_HUMAN	Nuclear factor of activated T-cells 5 (T-cell transcription factor NFAT5) (NF-AT5) (Tonicity-respons ...	0.92	-	nuc	0	Nucleus	nucleus [TAS]	604708	1IMH	1531
Q5F2E7 UniProt NPD GO	NUFP2_MOUSE	Nuclear fragile X mental retardation-interacting protein 2 (FMRP-interacting protein 2) (82 kDa FMRP ...	0.92	-	nuc	0	Nucleus. Cytoplasm. Localized in both nucleus and cytoplasm in most neurons. In the cortex, distribu ...				692
Q7Z417 UniProt NPD GO	NUFP2_HUMAN	Nuclear fragile X mental retardation-interacting protein 2 (FMRP-interacting protein 2) (82 kDa FMRP ...	0.92	-	nuc	0	Nucleus. Cytoplasm. Distribution is cell cycle-modulated, being cytoplasmic in the G2/M phase and ac ...		609356		695
O01929 UniProt NPD GO	NH153_CAEEL	Nuclear hormone receptor family member nhr-153	0.92	-	nuc	0	Nucleus (Potential)				415
Q61LN7 UniProt NPD GO	NOC3L_CAEBR	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.92	-	nuc	0	Nucleus; nucleolus (By similarity)				779
P41777 UniProt NPD GO	NOLC1_RAT	Nucleolar phosphoprotein p130 (Nucleolar 130 kDa protein) (140 kDa nucleolar phosphoprotein) (Nopp14 ...	0.92	+	nuc	0	Cytoplasm. Nucleus; nucleolus. Shuttles on curvilinear tracks between nucleolus and cytoplasm. These ...				704
Q4IQW0 UniProt NPD GO	NOP12_GIBZE	Nucleolar protein 12	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)				559

You are viewing entries 3301 to 3350 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.)

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