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
Q10146 UniProt NPD GO	YD81_SCHPO	Hypothetical protein C1F3.01 in chromosome I	0.90	-	nuc	0					777
Q10304 UniProt NPD GO	YD4B_SCHPO	Hypothetical protein C22H10.11c in chromosome I	0.90	-	nuc	0					629
Q09699 UniProt NPD GO	YA28_SCHPO	Hypothetical protein C2F7.08c in chromosome I	0.90	+	nuc	0					632
Q03568 UniProt NPD GO	YLD3_CAEEL	Hypothetical protein C38C10.3	0.90	-	nuc	0					301
O14216 UniProt NPD GO	YDTB_SCHPO	Hypothetical protein C6B12.11 in chromosome I	0.90	-	nuc	0		nucleus [IDA]			337
Q9W3C2 UniProt NPD GO	GSCR2_DROME	Hypothetical protein CG1785	0.90	+	nuc	0					478
Q09385 UniProt NPD GO	YMWB_CAEEL	Hypothetical protein K04G7.11	0.90	+	nuc	0					234
P34511 UniProt NPD GO	YMX3_CAEEL	Hypothetical protein K06H7.3	0.90	+	nuc	0					618
Q23525 UniProt NPD GO	YWIE_CAEEL	Hypothetical protein ZK546.14 in chromosome II	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				472
Q28224 UniProt NPD GO	IRS1_CERAE	Insulin receptor substrate 1 (IRS-1)	0.90	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			1251
P35569 UniProt NPD GO	IRS1_MOUSE	Insulin receptor substrate 1 (IRS-1)	0.90	-	nuc	0		cytoplasm [IDA] microsome [IDA] nucleus [IDA]		1AYB	1233
P35570 UniProt NPD GO	IRS1_RAT	Insulin receptor substrate 1 (IRS-1) (pp185)	0.90	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			1235
P84770 UniProt NPD GO	IRS1B_XENLA	Insulin receptor substrate 1-B (IRS1-B) (xIRS-1-B) (XIRS-L')	0.90	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			1088
Q8UVC1 UniProt NPD GO	INVS_BRARE	Inversin	0.90	+	nuc	0	Cytoplasm (By similarity). Associates with the cytoskeleton (By similarity)				1021
Q71S21 UniProt NPD GO	INVSB_XENLA	Inversin-B	0.90	-	nuc	0	Cytoplasm (By similarity). Associates with the cytoskeleton (By similarity)				1002
Q61768 UniProt NPD GO	KINH_MOUSE	Kinesin heavy chain (Ubiquitous kinesin heavy chain) (UKHC)	0.90	-	nuc	0	Uniformly distributed between soma and neurites in hippocampal neurons (By similarity)	ciliary rootlet [IDA] cytoplasm [IDA] kinesin complex [TAS] neuron projection [IDA]			963
P28742 UniProt NPD GO	KIP1_YEAST	Kinesin-like protein KIP1 (Chromosome instability protein 9)	0.90	+	mit	0	Spindle. Spindle microtubules that lie between the poles	kinesin complex [TAS] spindle microtubule [TAS] spindle pole body [IDA]			1111
Q91783 UniProt NPD GO	EG52_XENLA	Kinesin-related motor protein Eg5 2	0.90	-	nuc	0	Cytoplasm. Concentrated around the polar ends of both meiotic and mitotic spindles				1067
P14733 UniProt NPD GO	LMNB1_MOUSE	Lamin-B1	0.90	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side	lamin filament [IDA] nucleus [IDA]			587
P21619 UniProt NPD GO	LMNB2_MOUSE	Lamin-B2	0.90	+	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side	lamin filament [IDA]			596
Q61029 UniProt NPD GO	LAP2B_MOUSE	Lamina-associated polypeptide 2 isoforms beta/delta/epsilon/gamma (Thymopoietin isoforms beta/delta/ ...	0.90	+	nuc	1	Nucleus; nuclear inner membrane; single-pass type II membrane protein (By similarity). Tightly assoc ...	nuclear envelope [IDA]			451
P60853 UniProt NPD GO	LZTS1_MOUSE	Leucine zipper putative tumor suppressor 1 (F37/Esophageal cancer-related gene-coding leucine-zipper ...	0.90	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Associated with the plasma membrane and wi ...				598
Q5S006 UniProt NPD GO	LRRK2_MOUSE	Leucine-rich repeat serine/threonine-protein kinase 2 (EC 2.7.11.1)	0.90	-	nuc	0					2527
O88978 UniProt NPD GO	LRRC6_MOUSE	Leucine-rich repeat-containing protein 6 (Leucine-rich testis-specific protein) (Testis-specific leu ...	0.90	-	nuc	0	Cytoplasm				473
P08575 UniProt NPD GO	CD45_HUMAN	Leukocyte common antigen precursor (EC 3.1.3.48) (L-CA) (CD45 antigen) (T200)	0.90	-	exc	2	Membrane; single-pass type I membrane protein	focal adhesion [ISS] integral to plasma membrane [ISS]	151460	1YGU	1304
P27782 UniProt NPD GO	LEF1_MOUSE	Lymphoid enhancer-binding factor 1 (LEF-1)	0.90	+	nuc	0	Nucleus. Found in nuclear bodies upon PIASG binding	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IPI]		2LEF	397
Q99550 UniProt NPD GO	MPP9_HUMAN	M-phase phosphoprotein 9	0.90	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (Probable)	Golgi apparatus [TAS]	605501		692
Q8N3R9 UniProt NPD GO	MPP5_HUMAN	MAGUK p55 subfamily member 5	0.90	+	nuc	0	Cell membrane; peripheral membrane protein. Intracellular membrane; peripheral membrane protein. Loc ...		606958	1Y76	675
Q5RDQ2 UniProt NPD GO	MPP5_PONPY	MAGUK p55 subfamily member 5	0.90	+	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Intracellular membrane; peripheral membr ...				675
P93203 UniProt NPD GO	MFP1_LYCES	MAR-binding filament-like protein 1	0.90	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix				697
Q9ULH7 UniProt NPD GO	MKL2_HUMAN	MKL/myocardin-like protein 2 (Myocardin-related transcription factor B) (MRTF-B) (Megakaryoblastic l ...	0.90	-	nuc	0	Nucleus (By similarity)	nucleus [IC]	609463		1088
Q8TE76 UniProt NPD GO	MORC4_HUMAN	MORC family CW-type zinc finger 4 (Zinc finger CW-type coiled-coil domain protein 2)	0.90	+	nuc	0					937
Q8WJV2 UniProt NPD GO	MATK_DRACH	Maturase K (Intron maturase)	0.90	-	mit	0	Plastid; chloroplast				517
Q9GHB8 UniProt NPD GO	MATK_PHATN	Maturase K (Intron maturase)	0.90	-	nuc	0	Plastid; chloroplast				516
Q8M986 UniProt NPD GO	MATK_PLAAE	Maturase K (Intron maturase)	0.90	-	cyt	0	Plastid; chloroplast				514
Q9TIQ4 UniProt NPD GO	MATK_VERAR	Maturase K (Intron maturase)	0.90	-	nuc	0	Plastid; chloroplast				517
Q8WJR9 UniProt NPD GO	MATK_ARPGI	Maturase K (Intron maturase) (Fragment)	0.90	-	cyt	0	Plastid; chloroplast				509
Q9WVQ1 UniProt NPD GO	MAGI2_MOUSE	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (Membrane-associated gu ...	0.90	+	nuc	0	Synaptosome; peripheral membrane protein (By similarity). Membrane-associated in synaptosomes (By si ...				1275
Q02395 UniProt NPD GO	MTF2_MOUSE	Metal-response element-binding transcription factor 2 (Zinc-regulated factor 1) (ZiRF1) (Metal-respo ...	0.90	+	nuc	0	Nucleus				593
Q8K4B0 UniProt NPD GO	MTA1_MOUSE	Metastasis-associated protein MTA1	0.90	+	nuc	0	Nucleus	nucleus [IDA]			715
Q00566 UniProt NPD GO	MECP2_RAT	Methyl-CpG-binding protein 2 (MeCP-2 protein) (MeCP2)	0.90	+	nuc	0	Nucleus. Colocalized with methyl-CpG in the genome				492
Q9Y2H9 UniProt NPD GO	MAST1_HUMAN	Microtubule-associated serine/threonine-protein kinase 1 (EC 2.7.11.1) (Syntrophin-associated serine ...	0.90	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Colocalizes with syntrophins at the cell ...				1570
P46743 UniProt NPD GO	RT04_PROWI	Mitochondrial ribosomal protein S4	0.90	-	nuc	0	Mitochondrion				511
Q61083 UniProt NPD GO	M3K2_MOUSE	Mitogen-activated protein kinase kinase kinase 2 (EC 2.7.11.25) (MAPK/ERK kinase kinase 2) (MEK kina ...	0.90	-	nuc	0	Cytoplasm. Upon EGF stimulation, translocates into the nucleus				619
Q09591 UniProt NPD GO	MIX1_CAEEL	Mitotic chromosome and X-chromosome-associated protein mix-1 (Structural maintenance of chromosome 2 ...	0.90	+	nuc	0	Nucleus. Specifically associates with the X chromosome in both males and hermaphrodites in interphas ...	condensed chromosome [IDA]			1244
Q9U7D5 UniProt NPD GO	ACM3_CAEEL	Muscarinic acetylcholine receptor gar-3 (G-protein linked acetylcholine receptor 3)	0.90	-	nuc	7	Membrane; multi-pass membrane protein				611
P06171 UniProt NPD GO	MYC1_XENLA	Myc-A protein (Myc I protein) (C-Myc I)	0.90	+	nuc	0	Nucleus				419
P15171 UniProt NPD GO	MYCB_XENLA	Myc-B protein (Myc II protein) (C-Myc II)	0.90	+	nuc	0	Nucleus				420
Q01538 UniProt NPD GO	MYT1_HUMAN	Myelin transcription factor 1 (MyT1) (MyTI) (Proteolipid protein-binding protein) (PLPB1)	0.90	+	nuc	0	Nucleus	nucleus [NAS]	600379		1121
Q9UMN6 UniProt NPD GO	MLL4_HUMAN	Myeloid/lymphoid or mixed-lineage leukemia protein 4 (Trithorax homolog 2)	0.90	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]	606834		2715

You are viewing entries 4201 to 4250 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.