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
P35900 UniProt NPD GO	K1C20_HUMAN	Keratin, type I cytoskeletal 20 (Cytokeratin-20) (CK-20) (Keratin-20) (K20) (Protein IT)	0.48	-	mit	0	Cytoplasm	intermediate filament [NAS]	608218		424
P12035 UniProt NPD GO	K2C3_HUMAN	Keratin, type II cytoskeletal 3 (Cytokeratin-3) (CK-3) (Keratin-3) (K3) (65 kDa cytokeratin)	0.48	+	cyt	0		keratin filament [TAS]	148043		629
P07744 UniProt NPD GO	K2C4_MOUSE	Keratin, type II cytoskeletal 4 (Cytokeratin-4) (CK-4) (Keratin-4) (K4) (Cytoskeletal 57 kDa keratin ...	0.48	-	cyt	0		keratin filament [TAS]			525
P04266 UniProt NPD GO	K2C1_XENLA	Keratin, type II cytoskeletal I (Clone PUF23) (Fragment)	0.48	-	cyt	0					425
P25691 UniProt NPD GO	K2M3_SHEEP	Keratin, type II microfibrillar, component 5	0.48	-	mit	0					502
Q9BYR0 UniProt NPD GO	KRA47_HUMAN	Keratin-associated protein 4-7 (Keratin-associated protein 4.7) (Ultrahigh sulfur keratin-associated ...	0.48	-	nuc	0					210
Q64329 UniProt NPD GO	KLRA3_MOUSE	Killer cell lectin-like receptor 3 (T-cell surface glycoprotein Ly-49C) (Ly49-C antigen) (Lymphocyte ...	0.48	+	nuc	1 *	Membrane; single-pass type II membrane protein			1P4L	266
P70188 UniProt NPD GO	KIFA3_MOUSE	Kinesin-associated protein 3 (KAP3)	0.48	+	nuc	0		kinesin II complex [IPI]			793
Q9UEF7 UniProt NPD GO	KLOT_HUMAN	Klotho precursor (EC 3.2.1.31) [Contains: Klotho peptide]	0.48	-	gol	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Its shedding leads to a soluble pepti ...		604824		1012
Q99MZ8 UniProt NPD GO	LASP1_RAT	LIM and SH3 domain protein 1 (LASP-1)	0.48	-	nuc	0	Cytoplasm. Associated with the F-actin rich cortical cytoskeleton	cortical actin cytoskeleton [IDA]			263
Q9LQR0 UniProt NPD GO	LBD1_ARATH	LOB domain-containing protein 1	0.48	-	nuc	0					190
Q9SLB7 UniProt NPD GO	LBD16_ARATH	LOB domain-containing protein 16	0.48	-	nuc	0					245
P97927 UniProt NPD GO	LAMA4_MOUSE	Laminin alpha-4 chain precursor	0.48	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basal lamina [IDA]			1816
Q969R5 UniProt NPD GO	LMBL2_HUMAN	Lethal(3)malignant brain tumor-like 2 protein (L(3)mbt-like 2 protein) (H-l(3)mbt-like protein)	0.48	+	mit	0	Nucleus (Probable)	nucleus [NAS]			705
Q6AXL3 UniProt NPD GO	LRC33_BRARE	Leucine-rich repeat-containing protein 33 precursor	0.48	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				685
Q8BGI7 UniProt NPD GO	LRC39_MOUSE	Leucine-rich repeat-containing protein 39	0.48	-	nuc	0					337
Q7SXW3 UniProt NPD GO	LRC40_BRARE	Leucine-rich repeat-containing protein 40	0.48	-	nuc	0					601
Q9CRC8 UniProt NPD GO	LRC40_MOUSE	Leucine-rich repeat-containing protein 40	0.48	-	nuc	0					602
Q6GPJ5 UniProt NPD GO	LRC40_XENLA	Leucine-rich repeat-containing protein 40	0.48	-	nuc	0					605
Q5FVI3 UniProt NPD GO	LRC57_RAT	Leucine-rich repeat-containing protein 57	0.48	-	nuc	0					239
Q6INV3 UniProt NPD GO	LRC57_XENLA	Leucine-rich repeat-containing protein 57	0.48	-	nuc	0					238
Q8TDW0 UniProt NPD GO	LRC8C_HUMAN	Leucine-rich repeat-containing protein 8C (Protein AD158)	0.48	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				803
Q8LW53 UniProt NPD GO	CHLN_CHAGL	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.48	+	cyt	0	Plastid; chloroplast				458
P31995 UniProt NPD GO	FCG2C_HUMAN	Low affinity immunoglobulin gamma Fc region receptor II-c precursor (Fc-gamma RII-c) (FcRII-c) (IgG ...	0.48	-	exc	1	Isoform IIC1, isoform IIC2, isoform IIC3: Cell membrane; single-pass type I membrane protein. Isofor ...	integral to membrane [NAS]			323
P20063 UniProt NPD GO	LDLR_RABIT	Low-density lipoprotein receptor (LDL receptor) (Fragment)	0.48	-	nuc	1	Membrane; single-pass type I membrane protein				837
Q91VN0 UniProt NPD GO	LRP5_MOUSE	Low-density lipoprotein receptor-related protein 5 precursor (LRP7) (Lr3)	0.48	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	mitochondrion [IDA]			1614
Q95L39 UniProt NPD GO	LOXL1_BOVIN	Lysyl oxidase homolog 1 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 1)	0.48	-	nuc	0	Secreted protein; extracellular space (Potential)				591
P22670 UniProt NPD GO	RFX1_HUMAN	MHC class II regulatory factor RFX1 (RFX) (Enhancer factor C) (EF-C)	0.48	+	nuc	0	Nucleus		600006	1DP7	979
P43563 UniProt NPD GO	MOB2_YEAST	Maintenance of ploidy protein MOB2 (MPS1 binder 2)	0.48	-	mit	0	Nucleus. Cytoplasm. Localizes to the bud cortex during polarized growth and to the bud neck and daug ...	bud neck [IDA] mating projection tip [TAS] nucleus [IDA]			259
P23642 UniProt NPD GO	VAN1_YEAST	Mannan polymerase I complex VAN1 subunit (M-pol I subunit VAN1) (Vanadate resistance protein)	0.48	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	alpha-1,6-mannosyltransferase complex [IDA] Golgi cis-face [TAS] membrane [TAS]			535
Q5YJX3 UniProt NPD GO	MATK_GYMDI	Maturase K (Intron maturase)	0.48	-	cyt	0	Plastid; chloroplast				499
Q99640 UniProt NPD GO	PMYT1_HUMAN	Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (EC 2.7.11.1) (Myt1 kina ...	0.48	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Golgi apparatus; ...	endoplasmic reticulum [TAS] Golgi apparatus [TAS] membrane fraction [TAS]	602474		499
O00222 UniProt NPD GO	MGR8_HUMAN	Metabotropic glutamate receptor 8 precursor (mGluR8)	0.48	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601116		908
P82650 UniProt NPD GO	RT22_HUMAN	Mitochondrial 28S ribosomal protein S22 (S22mt) (MRP-S22)	0.48	-	mit	0	Mitochondrion	mitochondrial ribosome [NAS]	605810		360
P33441 UniProt NPD GO	MFT1_YEAST	Mitochondrial fusion target protein	0.48	-	nuc	0		THO complex [IMP]			392
Q6BN05 UniProt NPD GO	MG101_DEBHA	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.48	+	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				275
Q01992 UniProt NPD GO	PMIP_RAT	Mitochondrial intermediate peptidase, mitochondrial precursor (EC 3.4.24.59) (MIP)	0.48	-	mit	0	Mitochondrion; mitochondrial matrix				710
Q5VN19 UniProt NPD GO	MPK11_ORYSA	Mitogen-activated protein kinase 11 (EC 2.7.11.24) (MAP kinase 11)	0.48	-	cyt	0					570
Q5VP69 UniProt NPD GO	MPK16_ORYSA	Mitogen-activated protein kinase 16 (EC 2.7.11.24) (MAP kinase 16)	0.48	-	cyt	0					501
P26448 UniProt NPD GO	BUB2_YEAST	Mitotic check point protein BUB2 (Cell cycle arrest protein BUB2)	0.48	-	nuc	1	Spindle poles	spindle pole body [IDA]			306
P37202 UniProt NPD GO	DIS3_SCHPO	Mitotic control protein dis3	0.48	-	nuc	0	Cytoplasm. Nucleus. Abundant in the nucleus	nucleus [IDA]			970
P60762 UniProt NPD GO	MO4L1_MOUSE	Mortality factor 4-like protein 1 (MORF-related gene 15 protein) (Transcription factor-like protein ...	0.48	-	nuc	0	Nucleus (By similarity)	chromatin remodeling complex [TAS]			362
Q5EAA4 UniProt NPD GO	MOL2C_BOVIN	Mps one binder kinase activator-like 2C (Mob1 homolog 2C)	0.48	-	nuc	0					216
Q60528 UniProt NPD GO	MUC1_MESAU	Mucin-1 precursor	0.48	-	exc	1	Membrane; single-pass type I membrane protein				676
Q8N387 UniProt NPD GO	MUC15_HUMAN	Mucin-15 precursor	0.48	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...		608566		334
Q00449 UniProt NPD GO	MDR49_DROME	Multidrug resistance protein homolog 49 (EC 3.6.3.44) (P-glycoprotein 49)	0.48	+	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [NAS]			1302
P28666 UniProt NPD GO	MUG2_MOUSE	Murinoglobulin-2 precursor (MuG2)	0.48	-	mit	0	Secreted protein				1451
P10569 UniProt NPD GO	MYSC_ACACA	Myosin IC heavy chain	0.48	+	nuc	0					1168
Q9NXH9 UniProt NPD GO	TRM1_HUMAN	N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2)) methylt ...	0.48	-	mit	0					659
P25464 UniProt NPD GO	ACVS_CEPAC	N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase (EC 6.3.2.26) (Delta-(L-alpha-aminoadip ...	0.48	-	nuc	0					3712

You are viewing entries 26351 to 26400 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.