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
Q9HA64 UniProt NPD GO	KT3K_HUMAN	Ketosamine-3-kinase (EC 2.7.1.-) (Fructosamine-3-kinase-related protein)	0.10	-	cyt	0					309
Q924U1 UniProt NPD GO	KISSR_RAT	KiSS-1 receptor (KiSS-1R) (Kisspeptins receptor) (Metastin receptor) (G-protein coupled receptor 54) ...	0.10	-	end	6 *	Membrane; multi-pass membrane protein				396
P83057 UniProt NPD GO	KNL2_BOMVA	Kininogen-2 precursor (BVK-2) [Contains: [Val1,Thr3,Thr6]-bradykinin; Kininogen-2-associated peptide ...	0.10	-	exc	0	Secreted protein				96
Q924S4 UniProt NPD GO	KREM1_RAT	Kremen protein 1 precursor (Kringle-containing protein marking the eye and the nose) (Kringle domain ...	0.10	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS]			473
Q9TWG0 UniProt NPD GO	KC1_ANESU	Kunitz-type kalicludin-1 (AsKC1) (Kalicludine-1)	0.10	-	nuc	0	Secreted protein. Found in nematocyst				58
P81129 UniProt NPD GO	ISH2_STOHE	Kunitz-type proteinase inhibitor SHPI-2	0.10	-	cyt	0	Secreted protein. Found in nematocyst				55
P81382 UniProt NPD GO	OXLA_AGKRH	L-amino-acid oxidase precursor (EC 1.4.3.2) (LAO) (LAAO) (Apoxin I)	0.10	-	end	0	Secreted protein			1F8S	516
Q6FMI5 UniProt NPD GO	LYS2_CANGA	L-aminoadipate-semialdehyde dehydrogenase large subunit (EC 1.2.1.31) (Alpha-aminoadipate reductase) ...	0.10	-	mit	0					1374
P48534 UniProt NPD GO	APX1_PEA	L-ascorbate peroxidase, cytosolic (EC 1.11.1.11) (AP)	0.10	-	nuc	0	Cytoplasm			1APX	249
P38986 UniProt NPD GO	ASPG1_YEAST	L-asparaginase 1 (EC 3.5.1.1) (L-asparaginase I) (L-asparagine amidohydrolase I) (ASP I)	0.10	-	cyt	0	Cytoplasm	intracellular [IDA]			381
Q12541 UniProt NPD GO	LAC1_AGABI	Laccase-1 precursor (EC 1.10.3.2) (Laccase I) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) ...	0.10	-	exc	0	Secreted protein				520
Q6KB55 UniProt NPD GO	SIAT9_PANTR	Lactosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.9) (CMP-NeuAc:lactosylceramide alpha-2,3-sia ...	0.10	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				362
Q27262 UniProt NPD GO	LAMB1_HYDAT	Laminin beta-1 chain precursor (Fragments)	0.10	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component				171
P51093 UniProt NPD GO	LDOX_VITVI	Leucoanthocyanidin dioxygenase (EC 1.14.11.19) (LDOX) (Leucocyanidin oxygenase) (Leucoanthocyanidin ...	0.10	-	nuc	0					362
P11325 UniProt NPD GO	SYLM_YEAST	Leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			894
P31053 UniProt NPD GO	CD37_RAT	Leukocyte antigen CD37	0.10	-	end	4 *	Membrane; multi-pass membrane protein				281
Q85WT6 UniProt NPD GO	CHLL_PINKO	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.10	-	nuc	0	Plastid; chloroplast				291
P37853 UniProt NPD GO	CHLB_PICMA	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.10	-	mit	0	Plastid; chloroplast				104
Q13449 UniProt NPD GO	LSAMP_HUMAN	Limbic system-associated membrane protein precursor (LSAMP)	0.10	-	end	1	Cell membrane; lipid-anchor; GPI-anchor		603241		338
O94091 UniProt NPD GO	LIP1_CANAL	Lipase 1 precursor (EC 3.1.1.3)	0.10	-	exc	0	Secreted protein				468
Q9VXY7 UniProt NPD GO	LSD2_DROME	Lipid storage droplets surface-binding protein 2 (Lsd2)	0.10	-	nuc	0	Cytoplasm. Cytoplasm and on surface of neutral lipid storage droplets in oocytes. Colocalizes with L ...	lipid particle [IDA]			352
Q06000 UniProt NPD GO	LIPL_RAT	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.10	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				474
P01384 UniProt NPD GO	NXL1_NOTSC	Long neurotoxin 1 (Notechis III-4)	0.10	-	nuc	0	Secreted protein				73
Q6PCB7 UniProt NPD GO	S27A1_HUMAN	Long-chain fatty acid transport protein 1 (EC 6.2.1.-) (Fatty acid transport protein 1) (FATP-1) (So ...	0.10	-	exc	1 *	Cell membrane; peripheral membrane protein. Intracellular membrane; peripheral membrane protein. Pla ...		600691		646
Q5K4L6 UniProt NPD GO	S27A3_HUMAN	Long-chain fatty acid transport protein 3 (EC 6.2.1.-) (Fatty acid transport protein 3) (FATP-3) (Ve ...	0.10	-	end	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)		604193		683
Q91VE0 UniProt NPD GO	S27A4_MOUSE	Long-chain fatty acid transport protein 4 (EC 6.2.1.-) (Fatty acid transport protein 4) (FATP-4) (So ...	0.10	-	mit	2 *	Membrane; multi-pass membrane protein (Probable)	plasma membrane [TAS]			643
Q9Y2P4 UniProt NPD GO	S27A6_HUMAN	Long-chain fatty acid transport protein 6 (Fatty acid transport protein 6) (FATP-6) (Very long-chain ...	0.10	-	end	0	Membrane; multi-pass membrane protein (Potential). In heart is exclusively located on the sarcolemma ...		604196		619
P79274 UniProt NPD GO	ACADL_PIG	Long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.13) (LCAD)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				430
Q7KRI2 UniProt NPD GO	LOLAL_DROME	Longitudinals lacking protein-like (Lola-like protein) (Batman protein)	0.10	-	cyt	0	Nucleus	condensed nuclear chromosome [IDA] nucleus [IDA] PcG protein complex [IPI] polytene chromosome [IDA]			127
Q8S8H3 UniProt NPD GO	LCR5_ARATH	Low-molecular-weight cysteine-rich protein LCR5 precursor	0.10	-	exc	1 *					78
P33088 UniProt NPD GO	LSHB_BALAC	Lutropin beta chain (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.10	-	mit	0	Secreted protein				118
P80664 UniProt NPD GO	LSHB_STRCA	Lutropin beta chain (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.10	-	cyt	0	Secreted protein				128
Q8WN18 UniProt NPD GO	LSHB_AILME	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.10	-	nuc	0	Secreted protein				141
P01229 UniProt NPD GO	LSHB_HUMAN	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.10	-	mit	0	Secreted protein	soluble fraction [TAS]	152780	1M92	141
Q9BDI9 UniProt NPD GO	LSHB_PANTA	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.10	-	nuc	0	Secreted protein				142
Q2Q1P0 UniProt NPD GO	LSHB_PONPY	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.10	-	mit	0	Secreted protein				141
O95274 UniProt NPD GO	LYPD3_HUMAN	Ly6/PLAUR domain-containing protein 3 precursor (GPI-anchored metastasis-associated protein C4.4A ho ...	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [TAS]	609484		346
Q43503 UniProt NPD GO	LCYB_LYCES	Lycopene beta cyclase, chloroplast precursor (EC 1.14.-.-)	0.10	-	nuc	0	Plastid; chloroplast				500
P35459 UniProt NPD GO	LY6D_MOUSE	Lymphocyte antigen Ly-6D precursor (Thymocyte B-cell antigen) (ThB)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				127
P26445 UniProt NPD GO	TNFB_PIG	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.10	-	exc	1 *	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				204
Q9HBW0 UniProt NPD GO	EDG4_HUMAN	Lysophosphatidic acid receptor Edg-4 (LPA receptor 2) (LPA-2)	0.10	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605110		351
Q9PU16 UniProt NPD GO	LPA12_XENLA	Lysophosphatidic acid receptor LPA1 homolog 2 (xLPA1-2)	0.10	-	end	7	Membrane; multi-pass membrane protein				366
P39457 UniProt NPD GO	PLB1_PENCH	Lysophospholipase precursor (EC 3.1.1.5) (Phospholipase B) (Fragment)	0.10	-	cyt	0	Secreted protein				612
Q3MI05 UniProt NPD GO	PPGB_BOVIN	Lysosomal protective protein precursor (EC 3.4.16.5) [Contains: Lysosomal protective protein 32 kDa ...	0.10	-	exc	0	Lysosome (By similarity)				479
Q7YT16 UniProt NPD GO	LYS1_MUSDO	Lysozyme 1 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase 1)	0.10	-	exc	0					141
Q6B411 UniProt NPD GO	LYSM_BOVIN	Lysozyme C, milk isozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.10	-	vac	0					148
P40121 UniProt NPD GO	CAPG_HUMAN	Macrophage capping protein (Actin-regulatory protein CAP-G)	0.10	-	cyt	0	Cytoplasm. Nucleus	F-actin capping protein complex [TAS]	153615	1JHW	348
P10889 UniProt NPD GO	MIP2_MOUSE	Macrophage inflammatory protein 2 precursor (MIP2)	0.10	-	exc	0	Secreted protein			1MI2	100
Q9MUT3 UniProt NPD GO	CHLI_MESVI	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.10	-	nuc	0	Plastid; chloroplast				360
Q94FT3 UniProt NPD GO	CHLI_CHLRE	Magnesium-chelatase subunit chlI, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast stroma				417

You are viewing entries 64601 to 64650 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.