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
P01042 UniProt NPD GO	KNG1_HUMAN	Kininogen-1 precursor (Alpha-2-thiol proteinase inhibitor) [Contains: Kininogen-1 heavy chain; Brady ...	0.56	-	exc	0	Secreted protein; extracellular space	extracellular region [NAS]	228960		644
Q9JJZ6 UniProt NPD GO	KLF13_MOUSE	Krueppel-like factor 13 (Transcription factor BTEB3) (Basic transcription element-binding protein 3) ...	0.56	-	nuc	0	Nucleus				289
Q90476 UniProt NPD GO	LHX1_BRARE	LIM/homeobox protein Lhx1 (Homeobox protein LIM-1)	0.56	+	nuc	0	Nucleus (Potential)				405
P02469 UniProt NPD GO	LAMB1_MOUSE	Laminin beta-1 chain precursor (Laminin B1 chain)	0.56	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [IDA] laminin-1 [ISS]			1786
Q5TA76 UniProt NPD GO	LCE3A_HUMAN	Late cornified envelope protein 3A (Late envelope protein 13)	0.56	-	nuc	0					89
Q5T5B0 UniProt NPD GO	LCE3E_HUMAN	Late cornified envelope protein 3E (Late envelope protein 17)	0.56	-	nuc	0					92
P16889 UniProt NPD GO	H2BL3_STRPU	Late histone H2B.L3	0.56	+	nuc	0	Nucleus				122
Q8IYG6 UniProt NPD GO	LRC56_HUMAN	Leucine-rich repeat-containing protein 56	0.56	-	nuc	0					542
Q4V8C9 UniProt NPD GO	LRC56_RAT	Leucine-rich repeat-containing protein 56	0.56	-	nuc	0					548
P42702 UniProt NPD GO	LIFR_HUMAN	Leukemia inhibitory factor receptor precursor (LIF receptor) (LIF-R) (CD118 antigen)	0.56	-	nuc	1 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS]	601559		1097
Q8N423 UniProt NPD GO	LIRB2_HUMAN	Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor (Leukocyte immunoglobulin-like ...	0.56	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604815	2GW5	598
Q02200 UniProt NPD GO	PERX_NICSY	Lignin-forming anionic peroxidase precursor (EC 1.11.1.7)	0.56	-	exc	0	Secreted protein (By similarity)				322
Q9GZY6 UniProt NPD GO	NTAL_HUMAN	Linker for activation of T-cells family member 2 (Non-T-cell activation linker) (Linker for activati ...	0.56	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts	lipid raft [IDA]	605719		243
O88572 UniProt NPD GO	LRP6_MOUSE	Low-density lipoprotein receptor-related protein 6 precursor	0.56	-	end	1	Membrane; single-pass type I membrane protein (Potential)	membrane fraction [IDA]			1613
P33241 UniProt NPD GO	LSP1_HUMAN	Lymphocyte-specific protein 1 (Protein pp52) (52 kDa phosphoprotein) (Lymphocyte-specific antigen WP ...	0.56	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side	actin cytoskeleton [TAS]	153432		339
Q39685 UniProt NPD GO	CMB1_DIACA	MADS-box protein CMB1	0.56	-	nuc	0	Nucleus (By similarity)				233
Q655V4 UniProt NPD GO	MAD30_ORYSA	MADS-box transcription factor 30 (OsMADS30)	0.56	-	cyt	1	Nucleus (Probable)				221
P32491 UniProt NPD GO	MKK2_YEAST	MAP kinase kinase MKK2/SSP33 (EC 2.7.12.2)	0.56	-	nuc	0		intracellular [TAS]			506
P22897 UniProt NPD GO	MRC1_HUMAN	Macrophage mannose receptor 1 precursor (MMR) (CD206 antigen)	0.56	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	153618	1EGI	1456
Q96JY0 UniProt NPD GO	MAEL_HUMAN	Maelstrom homolog	0.56	-	nuc	0	Nucleus (Potential)			2CTO	434
Q9M591 UniProt NPD GO	CRD1_ARATH	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase, chloroplast precursor (EC 1.14.13. ...	0.56	-	mit	0	Plastid; chloroplast; chloroplast inner membrane; peripheral membrane protein. Plastid; chloroplast; ...				409
Q5EFU4 UniProt NPD GO	CRD1_HORVU	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase, chloroplast precursor (EC 1.14.13. ...	0.56	+	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Potential)				417
P54659 UniProt NPD GO	MVPB_DICDI	Major vault protein beta (MVP-beta)	0.56	-	cyt	0	Cytoplasm				846
P40744 UniProt NPD GO	B910_XENLA	Maternal B9.10 protein (P30 B9.10)	0.56	-	nuc	0					237
Q71U11 UniProt NPD GO	MATA2_CANAL	Mating-type-like protein A2 (MTLa2 protein)	0.56	-	mit	0	Nucleus (By similarity)				201
Q8MEE6 UniProt NPD GO	MATK_AMOPO	Maturase K (Intron maturase)	0.56	+	nuc	0	Plastid; chloroplast				512
Q9TN89 UniProt NPD GO	MATK_BEARE	Maturase K (Intron maturase)	0.56	-	cyt	0	Plastid; chloroplast				520
Q9TNB1 UniProt NPD GO	MATK_CONMJ	Maturase K (Intron maturase)	0.56	-	cyt	0	Plastid; chloroplast				520
Q6EIK6 UniProt NPD GO	MATK_GOSHI	Maturase K (Intron maturase)	0.56	-	nuc	0	Plastid; chloroplast				504
Q9XPN6 UniProt NPD GO	MATK_HELBU	Maturase K (Intron maturase)	0.56	-	cyt	0	Plastid; chloroplast				515
Q6QUK9 UniProt NPD GO	MATK_IDIAU	Maturase K (Intron maturase)	0.56	-	nuc	0	Plastid; chloroplast				505
Q8WHL7 UniProt NPD GO	MATK_LEMMI	Maturase K (Intron maturase)	0.56	-	nuc	0	Plastid; chloroplast				512
Q9MVD9 UniProt NPD GO	MATK_MICAL	Maturase K (Intron maturase)	0.56	-	cyt	0	Plastid; chloroplast				507
Q4H174 UniProt NPD GO	MATK_WATAN	Maturase K (Intron maturase)	0.56	-	cyt	0	Plastid; chloroplast				522
Q8MDU0 UniProt NPD GO	MATK_ABIBR	Maturase K (Intron maturase) (Fragment)	0.56	-	nuc	0	Plastid; chloroplast				508
P05728 UniProt NPD GO	MAT1_EUGGR	Maturase-like protein 1	0.56	-	cyt	0	Plastid; chloroplast				458
P43363 UniProt NPD GO	MAGAA_HUMAN	Melanoma-associated antigen 10 (MAGE-10 antigen)	0.56	-	nuc	0			300343		369
Q9ESG9 UniProt NPD GO	PMYT1_MOUSE	Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (EC 2.7.11.1) (Myt1 kina ...	0.56	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...				490
Q5U2R7 UniProt NPD GO	MESD2_RAT	Mesoderm development candidate 2	0.56	-	exc	0					224
Q68ED2 UniProt NPD GO	MGR7_MOUSE	Metabotropic glutamate receptor 7 precursor (mGluR7)	0.56	-	end	6	Membrane; multi-pass membrane protein	active zone presynaptic plasma membrane [TAS]			915
Q5RDQ8 UniProt NPD GO	MGR7_PONPY	Metabotropic glutamate receptor 7 precursor (mGluR7)	0.56	-	end	6	Membrane; multi-pass membrane protein (By similarity)				922
P35400 UniProt NPD GO	MGR7_RAT	Metabotropic glutamate receptor 7 precursor (mGluR7)	0.56	-	end	6	Membrane; multi-pass membrane protein				915
P32785 UniProt NPD GO	FMT_YEAST	Methionyl-tRNA formyltransferase, mitochondrial precursor (EC 2.1.2.9) (MtFMT)	0.56	-	mit	0	Mitochondrion	mitochondrion [IDA]			401
P36225 UniProt NPD GO	MAP4_BOVIN	Microtubule-associated protein 4 (MAP 4) (Microtubule-associated protein-U) (MAP-U)	0.56	-	nuc	0					1072
P82926 UniProt NPD GO	RT33_BOVIN	Mitochondrial 28S ribosomal protein S33 (S33mt) (MRP-S33)	0.56	-	nuc	0	Mitochondrion				106
Q6IQS9 UniProt NPD GO	RM23_BRARE	Mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23)	0.56	-	nuc	0	Mitochondrion (By similarity)				153
P32902 UniProt NPD GO	RT04_YEAST	Mitochondrial 40S ribosomal protein MRP4	0.56	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			394
P93311 UniProt NPD GO	RM02_ARATH	Mitochondrial 60S ribosomal protein L2	0.56	-	mit	0	Mitochondrion				349
P92812 UniProt NPD GO	RM02_ORYSA	Mitochondrial 60S ribosomal protein L2	0.56	-	mit	0	Mitochondrion				502
P48857 UniProt NPD GO	RT12_BRANA	Mitochondrial ribosomal protein S12	0.56	-	nuc	0	Mitochondrion				125

You are viewing entries 21451 to 21500 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.