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
Q9BYQ4 UniProt NPD GO	KRA92_HUMAN	Keratin-associated protein 9-2 (Keratin-associated protein 9.2) (Ultrahigh sulfur keratin-associated ...	0.46	-	mit	0					174
Q9NZU5 UniProt NPD GO	LMCD1_HUMAN	LIM and cysteine-rich domains protein 1 (Dyxin)	0.46	-	nuc	0			604859		365
P53669 UniProt NPD GO	LIMK1_RAT	LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1)	0.46	-	nuc	0	Cytoplasm. Localizes to the growth cone in hippocampal neurons				647
Q8QFP8 UniProt NPD GO	LIMK1_CHICK	LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1) (chLIMK1)	0.46	-	nuc	0	Cytoplasm. Recruited to axon growth cones				662
Q9JKS4 UniProt NPD GO	LDB3_MOUSE	LIM domain-binding protein 3 (Z-band alternatively spliced PDZ-motif protein) (Protein cypher) (Prot ...	0.46	-	nuc	0	Localized to the cytoplasm around nuclei and pseudopodia of undifferentiated cells and detected thro ...	cytoskeleton [ISS]		1WJL	723
O35652 UniProt NPD GO	LHX8_MOUSE	LIM/homeobox protein Lhx8 (LIM homeodomain Lhx7) (L3)	0.46	-	nuc	0	Nucleus (Probable)				367
Q9SJW5 UniProt NPD GO	LBD14_ARATH	LOB domain-containing protein 14	0.46	-	nuc	0					188
Q8CG18 UniProt NPD GO	LTB1S_MOUSE	Latent-transforming growth factor beta-binding protein, isoform 1S precursor (LTBP-1) (Transforming ...	0.46	-	nuc	0	Secreted protein (By similarity)	extracellular matrix (sensu Metazoa) [IDA]			1389
Q5XNR9 UniProt NPD GO	LIFR_CANFA	Leukemia inhibitory factor receptor precursor (LIF receptor) (LIF-R) (CD118 antigen)	0.46	-	nuc	1 *	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted p ...				1097
P59901 UniProt NPD GO	LIRA4_HUMAN	Leukocyte immunoglobulin-like receptor subfamily A member 4 precursor (Immunoglobulin-like transcrip ...	0.46	-	exc	0	Membrane; single-pass type I membrane protein		607517		499
O94691 UniProt NPD GO	JMJ3_SCHPO	Lid2 complex component jmj3 (Lid2C component jmj3)	0.46	-	nuc	0	Nucleus (Probable)	Lid2 complex [IDA]			752
Q9Y234 UniProt NPD GO	LIPB_HUMAN	Lipoyltransferase 1, mitochondrial precursor (EC 6.-.-.-) (Lipoate-protein ligase) (Lipoate biosynth ...	0.46	-	cyt	0	Mitochondrion				373
Q8C142 UniProt NPD GO	ARH_MOUSE	Low density lipoprotein receptor adapter protein 1 (Autosomal recessive hypercholesterolemia protein ...	0.46	-	cyt	0	Cytoplasm	basal plasma membrane [ISS] cytosol [ISS] early endosome [IDA]			308
O46432 UniProt NPD GO	MA2B1_FELCA	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha-man ...	0.46	-	cyt	0	Lysosome				1007
Q5NCE8 UniProt NPD GO	MRS2L_MOUSE	Magnesium transporter MRS2L, mitochondrial precursor (MRS2-like protein)	0.46	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				434
P51277 UniProt NPD GO	ACSF_PORPU	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (EC 1.14.13.81) (Mg-protoporphyrin ...	0.46	-	cyt	0	Plastid; chloroplast				349
Q945B7 UniProt NPD GO	CRD1_EUPES	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase, chloroplast precursor (EC 1.14.13. ...	0.46	-	cyt	0	Plastid; chloroplast (By similarity)				405
O35548 UniProt NPD GO	MMP16_RAT	Matrix metalloproteinase-16 precursor (EC 3.4.24.-) (MMP-16) (Membrane-type matrix metalloproteinase ...	0.46	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Localized at the cell surface of mel ...				607
Q5YK53 UniProt NPD GO	MATK_GLETR	Maturase K (Intron maturase)	0.46	-	cyt	0	Plastid; chloroplast				499
Q33078 UniProt NPD GO	MATK_SAXCE	Maturase K (Intron maturase) (Fragment)	0.46	-	cyt	0	Plastid; chloroplast				352
Q8JHE1 UniProt NPD GO	M3H5_BOMMX	Maximins 3/H5 precursor [Contains: Maximin-3; Maximin-H5]	0.46	-	exc	0	Secreted protein				144
O14220 UniProt NPD GO	MEU26_SCHPO	Meiotic expression up-regulated protein 26	0.46	-	nuc	0		nucleus [IDA]			344
Q9QXZ9 UniProt NPD GO	OPN4_MOUSE	Melanopsin (Opsin-4)	0.46	-	end	6	Membrane; multi-pass membrane protein. Found in soma, dendrites and proximal part of axons of certai ...				521
Q13255 UniProt NPD GO	MGR1_HUMAN	Metabotropic glutamate receptor 1 precursor (mGluR1)	0.46	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604473		1194
P23385 UniProt NPD GO	MGR1_RAT	Metabotropic glutamate receptor 1 precursor (mGluR1)	0.46	-	end	7	Membrane; multi-pass membrane protein	axon [IDA] integral to plasma membrane [TAS] presynaptic membrane [IDA]		1ISS	1199
Q5NCH9 UniProt NPD GO	MGR6_MOUSE	Metabotropic glutamate receptor 6 precursor (mGluR6)	0.46	-	end	6	Membrane; multi-pass membrane protein	postsynaptic membrane [TAS]			871
Q8N183 UniProt NPD GO	MIMIT_HUMAN	Mimitin, mitochondrial precursor (Myc-induced mitochondrial protein) (MMTN) (B17.2-like) (B17.2L)	0.46	-	nuc	0	Mitochondrion		609653		169
Q5B5L3 UniProt NPD GO	GEM1_EMENI	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.46	+	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				634
Q03713 UniProt NPD GO	YMD0_YEAST	Mitochondrial protein YML030W	0.46	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [IDA]			159
P51428 UniProt NPD GO	RT10_PEA	Mitochondrial ribosomal protein S10	0.46	-	cyt	0	Mitochondrion				110
Q9N272 UniProt NPD GO	MK13_PANTR	Mitogen-activated protein kinase 13 (EC 2.7.11.24) (Stress-activated protein kinase 4)	0.46	-	cyt	0					365
O15264 UniProt NPD GO	MK13_HUMAN	Mitogen-activated protein kinase 13 (EC 2.7.11.24) (Stress-activated protein kinase 4) (Mitogen-acti ...	0.46	-	cyt	0			602899		365
Q9UBU8 UniProt NPD GO	MO4L1_HUMAN	Mortality factor 4-like protein 1 (MORF-related gene 15 protein) (Transcription factor-like protein ...	0.46	-	nuc	0	Nucleus	nucleus [NAS]	607303	2AQL	362
P60207 UniProt NPD GO	CXM3A_CONSE	Mu-conotoxin SmIIIA precursor (Fragment)	0.46	-	nuc	0	Secreted protein				31
Q9HC84 UniProt NPD GO	MUC5B_HUMAN	Mucin-5B precursor (Mucin-5 subtype B, tracheobronchial) (High molecular weight salivary mucin MG1) ...	0.46	-	nuc	0	Secreted protein	extracellular region [NAS]	600770		5703
O15440 UniProt NPD GO	MRP5_HUMAN	Multidrug resistance-associated protein 5 (Multi-specific organic anion transporter-C) (MOAT-C) (pAB ...	0.46	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [IDA]	605251		1437
P17564 UniProt NPD GO	MY116_MOUSE	Myeloid differentiation primary response protein MyD116	0.46	-	nuc	0					657
Q99836 UniProt NPD GO	MYD88_HUMAN	Myeloid differentiation primary response protein MyD88	0.46	-	mit	0	Cytoplasm (Probable)		602170		296
P05164 UniProt NPD GO	PERM_HUMAN	Myeloperoxidase precursor (EC 1.11.1.7) (MPO) [Contains: 89 kDa myeloperoxidase; 84 kDa myeloperoxid ...	0.46	-	nuc	0	Lysosome	lysosome [TAS] nucleus [TAS]	254600	1MYP	745
Q2PT31 UniProt NPD GO	MYOC_CANFA	Myocilin precursor	0.46	-	exc	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...				483
O88329 UniProt NPD GO	MYO1A_MOUSE	Myosin Ia (Brush border myosin I) (BBM-I) (BBMI) (Myosin I heavy chain) (MIHC) (Fragment)	0.46	-	cyt	0					909
P15586 UniProt NPD GO	GL6S_HUMAN	N-acetylglucosamine-6-sulfatase precursor (EC 3.1.6.14) (G6S) (Glucosamine-6-sulfatase)	0.46	-	mit	1 *	Lysosome		607664		552
Q6BJY5 UniProt NPD GO	ECO1_DEBHA	N-acetyltransferase ECO1 (EC 2.3.1.-) (Establishment of cohesion protein 1)	0.46	-	nuc	0	Nucleus (By similarity)				288
P48305 UniProt NPD GO	NDUB4_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.46	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side				128
Q36450 UniProt NPD GO	NUCM_NICSY	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.46	-	cyt	0	Mitochondrion				394
Q96PH1 UniProt NPD GO	NOX5_HUMAN	NADPH oxidase 5 (EC 1.6.3.-)	0.46	-	end	7	Membrane; multi-pass membrane protein (Potential)		606572		765
Q8NFA2 UniProt NPD GO	NOXO1_HUMAN	NADPH oxidase organizer 1 (Nox organizer 1) (Nox-organizing protein 1) (NADPH oxidase regulatory pro ...	0.46	-	nuc	0	Isoform 3: Cell membrane; peripheral membrane protein; cytoplasmic side. Isoform 3 associates with t ...				376
Q9NPJ8 UniProt NPD GO	NXT2_HUMAN	NTF2-related export protein 2 (p15-2 protein)	0.46	-	cyt	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm		300320		142
P40753 UniProt NPD GO	ANFB_MOUSE	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic pepti ...	0.46	-	exc	0	Secreted protein				121
P16860 UniProt NPD GO	ANFB_HUMAN	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic pepti ...	0.46	-	exc	0	Secreted protein	extracellular region [TAS] extracellular space [NAS]	600295		134

You are viewing entries 27751 to 27800 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.