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
Q9NS61 UniProt NPD GO	KCIP2_HUMAN	Kv channel-interacting protein 2 (KChIP2) (A-type potassium channel modulatory protein 2) (Potassium ...	0.39	-	nuc	0	Isoform 1, isoform 2, isoform 6: Cell membrane; lipid-anchor (By similarity)		604661		270
Q9D6J1 UniProt NPD GO	LASS4_MOUSE	LAG1 longevity assurance homolog 4 (Translocating chain-associating membrane protein homolog 1) (TRA ...	0.39	-	end	6 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...	endoplasmic reticulum [IDA]			393
Q9Y4W2 UniProt NPD GO	LAS1L_HUMAN	LAS1-like protein	0.39	-	cyt	0	Nucleus; nucleolus				734
P53667 UniProt NPD GO	LIMK1_HUMAN	LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1)	0.39	-	nuc	0	Cytoplasm	cytoplasm [TAS]	601329		647
P59467 UniProt NPD GO	LBD23_ARATH	LOB domain-containing protein 23	0.39	-	nuc	0					121
O08984 UniProt NPD GO	LBR_RAT	Lamin-B receptor (Integral nuclear envelope inner membrane protein) (NBP60)	0.39	+	end	8	Nucleus; nuclear inner membrane; multi-pass membrane protein (By similarity)				620
Q8W1E0 UniProt NPD GO	R1A_SOLDE	Late blight resistance protein R1-A (Protein R1)	0.39	-	cyt	0	Cytoplasm (By similarity)				1293
P55796 UniProt NPD GO	LEB3_BOMMO	Lebocin-3 precursor (LEB 3)	0.39	-	mit	0	Secreted protein				179
P48357 UniProt NPD GO	LEPR_HUMAN	Leptin receptor precursor (LEP-R) (OB receptor) (OB-R) (HuB219) (CD295 antigen)	0.39	-	end	3 *	Cell membrane; single-pass type I membrane protein. Isoform E: Secreted protein (Probable)		601007		1165
P81829 UniProt NPD GO	LCK_DROME	Leucokinin precursor (DLK)	0.39	-	exc	0	Secreted protein				160
Q8N149 UniProt NPD GO	LIRA2_HUMAN	Leukocyte immunoglobulin-like receptor subfamily A member 2 precursor (Leukocyte immunoglobulin-like ...	0.39	-	exc	0	Membrane; single-pass type I membrane protein		604812		483
Q5U4X7 UniProt NPD GO	LMBR1_XENTR	Limb region 1 protein homolog	0.39	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				485
P39105 UniProt NPD GO	PLB1_YEAST	Lysophospholipase 1 precursor (EC 3.1.1.5) (Phospholipase B 1)	0.39	-	exc	0	Secreted protein	cell wall (sensu Fungi) [IDA]			664
Q11121 UniProt NPD GO	PLB1_TORDE	Lysophospholipase precursor (EC 3.1.1.5) (Phospholipase B)	0.39	-	mit	0	Secreted protein				649
P34810 UniProt NPD GO	CD68_HUMAN	Macrosialin precursor (GP110) (CD68 antigen)	0.39	-	exc	1	Isoform Long: Endosome; endosomal membrane; single-pass type I membrane protein. Isoform Long: Lysos ...	integral to membrane [TAS] membrane fraction [TAS]	153634		354
Q9SJE1 UniProt NPD GO	CHLD_ARATH	Magnesium-chelatase subunit chlD, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.39	-	mit	0	Plastid; chloroplast; chloroplast stroma				759
Q6PF69 UniProt NPD GO	MVP_XENLA	Major vault protein (MVP)	0.39	-	cyt	0	Cytoplasm (By similarity)				849
Q6DRP4 UniProt NPD GO	CCM2_BRARE	Malcavernin (Cerebral cavernous malformations protein 2 homolog)	0.39	-	nuc	0	Cytoplasm (By similarity)				455
Q800Y2 UniProt NPD GO	MGP_ARGRE	Matrix Gla-protein precursor (MGP)	0.39	-	exc	0	Secreted protein	extracellular matrix [IDA]			118
P08493 UniProt NPD GO	MGP_HUMAN	Matrix Gla-protein precursor (MGP)	0.39	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	245150		103
Q58T48 UniProt NPD GO	M3111_BOMMX	Maximins 3/H11 type 1 precursor [Contains: Maximin-3; Maximin-H11]	0.39	-	end	0	Secreted protein				144
Q58T65 UniProt NPD GO	M3113_BOMMX	Maximins 3/H11 type 3 precursor [Contains: Maximin-3; Maximin-H11]	0.39	-	end	0	Secreted protein				145
Q2TBN4 UniProt NPD GO	MED28_BOVIN	Mediator of RNA polymerase II transcription subunit 28 (Mediator complex subunit 28)	0.39	-	exc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane (By similarity). May be also cytoplasmi ...				178
Q920D3 UniProt NPD GO	MED28_MOUSE	Mediator of RNA polymerase II transcription subunit 28 (Mediator complex subunit 28)	0.39	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane (By similarity). May be also cytoplasmi ...				178
P24719 UniProt NPD GO	MEK1_YEAST	Meiosis-specific serine/threonine-protein kinase MEK1 (EC 2.7.11.1)	0.39	+	cyt	0		nucleus [IDA]			497
Q5XXP2 UniProt NPD GO	OPN4_PHOSU	Melanopsin (Opsin-4)	0.39	-	end	6	Membrane; multi-pass membrane protein. Found in soma, dendrites and proximal part of axons of retina ...				469
P14699 UniProt NPD GO	MAR2_LEIMA	Membrane antigen containing repeating peptides (Clone 20) (Fragment)	0.39	-	nuc	0					214
Q9WTZ3 UniProt NPD GO	MBTP1_RAT	Membrane-bound transcription factor site 1 protease precursor (EC 3.4.21.-) (S1P endopeptidase) (Sit ...	0.39	+	vac	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	Golgi apparatus [IDA]			1052
Q9WTZ2 UniProt NPD GO	MBTP1_MOUSE	Membrane-bound transcription factor site 1 protease precursor (EC 3.4.21.-) (S1P endopeptidase) (Sit ...	0.39	+	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	Golgi stack [IDA]			1052
Q99317 UniProt NPD GO	MSA2_PLAFC	Merozoite surface antigen 2 precursor (MSA-2) (Allelic form 1)	0.39	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				262
Q13421 UniProt NPD GO	MSLN_HUMAN	Mesothelin precursor (CAK1 antigen)	0.39	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. Not shed to the serum of cancer patients	membrane [NAS]	601051		628
P38356 UniProt NPD GO	BSD2_YEAST	Metal homeostatis protein BSD2	0.39	-	end	3	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] vacuolar membrane (sensu Fungi) [IDA]			321
Q5I598 UniProt NPD GO	MTHR_BOVIN	Methylenetetrahydrofolate reductase (EC 1.5.1.20)	0.39	-	cyt	0					655
O08601 UniProt NPD GO	MTP_MOUSE	Microsomal triglyceride transfer protein large subunit precursor	0.39	-	exc	0	Endoplasmic reticulum				894
Q7ZXP1 UniProt NPD GO	MARE2_XENLA	Microtubule-associated protein RP/EB family member 2	0.39	-	nuc	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				327
Q5S6V2 UniProt NPD GO	TAU_PONPY	Microtubule-associated protein tau	0.39	-	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Mostly found in the axons of neur ...	axon [ISS] cytosol [ISS] growth cone [ISS] microtubule associated complex [ISS] plasma membrane [ISS] tubulin [ISS]			757
P10637 UniProt NPD GO	TAU_MOUSE	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.39	-	nuc	0	Cytoplasm; cytosol. Cell membrane. Mostly found in the axons of neurons, in the cytosol and in assoc ...	axon [ISS] cytosol [ISS] growth cone [ISS] microtubule associated complex [ISS] plasma membrane [ISS] tubulin [ISS]			732
P82918 UniProt NPD GO	RT18B_BOVIN	Mitochondrial 28S ribosomal protein S18-2 (MRP-S18-2) (Mrps18b)	0.39	-	nuc	0	Mitochondrion				258
Q9Y399 UniProt NPD GO	RT02_HUMAN	Mitochondrial 28S ribosomal protein S2 (S2mt) (MRP-S2)	0.39	-	mit	0	Mitochondrion				296
Q9CXW2 UniProt NPD GO	RT22_MOUSE	Mitochondrial 28S ribosomal protein S22 (S22mt) (MRP-S22)	0.39	-	mit	0	Mitochondrion (By similarity)				359
Q16540 UniProt NPD GO	RM23_HUMAN	Mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23) (L23 mitochondrial-related protein) (Ribos ...	0.39	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]	600789		153
O21247 UniProt NPD GO	RM02_RECAM	Mitochondrial 60S ribosomal protein L2	0.39	-	nuc	0	Mitochondrion				277
Q00970 UniProt NPD GO	MG101_KLULA	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.39	+	mit	0					262
Q6BH37 UniProt NPD GO	TIM14_DEBHA	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.39	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				172
P46744 UniProt NPD GO	RT12_PROWI	Mitochondrial ribosomal protein S12	0.39	-	mit	0	Mitochondrion				125
P53070 UniProt NPD GO	MTO1_YEAST	Mitochondrial translation optimization protein, mitochondrial precursor	0.39	-	mit	0	Mitochondrion	mitochondrion [IDA]			679
Q920G8 UniProt NPD GO	MFRN1_MOUSE	Mitoferrin-1 (Mitochondrial iron transporter 1) (Solute carrier family 25 member 37) (Mitochondrial ...	0.39	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			338
Q7FNE2 UniProt NPD GO	MPK5_ORYSA	Mitogen-activated protein kinase 5 (EC 2.7.11.24) (MAP kinase 5) (OsMAPK5) (OsMAP1) (Benzothiadiazol ...	0.39	-	cyt	0					369
P40622 UniProt NPD GO	HMG1A_CHITE	Mobility group protein 1A	0.39	+	nuc	0	Nucleus				114
P84023 UniProt NPD GO	SMAD3_CHICK	Mothers against decapentaplegic homolog 3 (SMAD 3) (Mothers against DPP homolog 3) (Mad3)	0.39	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...				426

You are viewing entries 32751 to 32800 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.