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
Q04753 UniProt NPD GO	ICLN_RAT	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln)) (Chloride channel, ...	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytosol [IDA]			236
P54105 UniProt NPD GO	ICLN_HUMAN	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln)) (Chloride channel, ...	0.05	-	cyt	0	Cytoplasm. Nucleus. Cytoskeleton. A small fraction is also associated with the cytoskeleton	plasma membrane [TAS]	602158		237
Q5ZLC7 UniProt NPD GO	MARE1_CHICK	Microtubule-associated protein RP/EB family member 1	0.05	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				258
Q6V291 UniProt NPD GO	MARE1_COTCO	Microtubule-associated protein RP/EB family member 1	0.05	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				263
Q66T82 UniProt NPD GO	MARE1_COTJA	Microtubule-associated protein RP/EB family member 1	0.05	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				263
P13087 UniProt NPD GO	MIRA_RICDU	Miraculin precursor (MIR)	0.05	-	vac	1 *					220
Q02978 UniProt NPD GO	M2OM_HUMAN	Mitochondrial 2-oxoglutarate/malate carrier protein (OGCP) (Solute carrier family 25 member 11)	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to plasma membrane [TAS] mitochondrial inner membrane [TAS]	604165		313
P18665 UniProt NPD GO	RM03_RAT	Mitochondrial 39S ribosomal protein L3 (L3mt) (MRP-L3)	0.05	-	cyt	0	Mitochondrion				347
O21234 UniProt NPD GO	RM11_RECAM	Mitochondrial 60S ribosomal protein L11	0.05	-	nuc	0	Mitochondrion				145
P20084 UniProt NPD GO	RM33_YEAST	Mitochondrial 60S ribosomal protein L33 (YmL33)	0.05	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			85
P23500 UniProt NPD GO	MRS4_YEAST	Mitochondrial RNA-splicing protein MRS4	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			304
Q791V5 UniProt NPD GO	MTCH2_MOUSE	Mitochondrial carrier homolog 2	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]			303
Q9UBX3 UniProt NPD GO	DIC_HUMAN	Mitochondrial dicarboxylate carrier (Solute carrier family 25 member 10)	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		606794		287
Q6FTN2 UniProt NPD GO	DIC1_CANGA	Mitochondrial dicarboxylate transporter (Dicarboxylate carrier 1)	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				295
Q12036 UniProt NPD GO	PPT2_YEAST	Mitochondrial holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) (Mitochondrial holo-ACP synthase) (4 ...	0.05	-	cyt	0	Mitochondrion (Probable)	mitochondrion [IMP]			177
Q6CIK7 UniProt NPD GO	TIM10_KLULA	Mitochondrial import inner membrane translocase subunit TIM10	0.05	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
Q96DA6 UniProt NPD GO	TIM14_HUMAN	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 19)	0.05	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (Probable)		608977		115
Q5RF34 UniProt NPD GO	TIM14_PONPY	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 19)	0.05	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				115
P39515 UniProt NPD GO	TIM17_YEAST	Mitochondrial import inner membrane translocase subunit TIM17 (Mitochondrial protein import protein ...	0.05	-	mit	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane presequence tr... [IDA]			158
Q5M7K0 UniProt NPD GO	TIM22_XENTR	Mitochondrial import inner membrane translocase subunit Tim22	0.05	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				186
O14925 UniProt NPD GO	TIM23_HUMAN	Mitochondrial import inner membrane translocase subunit Tim23	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...	integral to membrane [TAS] mitochondrial inner membrane presequence tr... [TAS] mitochondrial intermembrane space [IDA]	605034		209
Q9WTQ8 UniProt NPD GO	TIM23_MOUSE	Mitochondrial import inner membrane translocase subunit Tim23	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...	mitochondrial inner membrane [IDA]			209
P87130 UniProt NPD GO	TIM17_SCHPO	Mitochondrial import inner membrane translocase subunit tim17 (Mitochondrial protein import protein ...	0.05	-	mit	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				164
Q12375 UniProt NPD GO	ORT1_YEAST	Mitochondrial ornithine carrier protein	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial envelope [IDA]			292
P23641 UniProt NPD GO	MPCP_YEAST	Mitochondrial phosphate carrier protein (Phosphate transport protein) (PTP) (mPic 1) (Mitochondrial ...	0.05	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial envelope [IDA] mitochondrion [IDA]			311
Q9W720 UniProt NPD GO	UCP2_BRARE	Mitochondrial uncoupling protein 2 (UCP 2)	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				310
P55851 UniProt NPD GO	UCP2_HUMAN	Mitochondrial uncoupling protein 2 (UCP 2) (UCPH)	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]	601693		309
P70406 UniProt NPD GO	UCP2_MOUSE	Mitochondrial uncoupling protein 2 (UCP 2) (UCPH)	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				309
P97997 UniProt NPD GO	MPPA_BLAEM	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane				474
Q5BLX8 UniProt NPD GO	MORG1_RAT	Mitogen-activated protein kinase organizer 1 (MAPK organizer 1)	0.05	-	cyt	0	Cytoplasm. Predominantly. Nucleus. Partially				315
Q9V8I2 UniProt NPD GO	MAPIP_DROME	Mitogen-activated protein-binding protein-interacting protein homolog	0.05	-	cyt	0					125
P53986 UniProt NPD GO	MOT1_MOUSE	Monocarboxylate transporter 1 (MCT 1)	0.05	-	end	11 *	Cell membrane; multi-pass membrane protein				493
P19863 UniProt NPD GO	MOTI_CANFA	Motilin	0.05	-	nuc	0	Secreted protein				22
P11060 UniProt NPD GO	TXMG4_AGEAP	Mu-agatoxin-4	0.05	-	nuc	0	Secreted protein			1EIV	37
P33535 UniProt NPD GO	OPRM_RAT	Mu-type opioid receptor (MOR-1) (Opioid receptor B) (MUOR1)	0.05	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [IDA]			398
Q09752 UniProt NPD GO	FNX1_SCHPO	Multidrug resistance protein fnx1	0.05	-	end	14 *	Membrane; multi-pass membrane protein (Probable)				531
Q9DCL9 UniProt NPD GO	PUR6_MOUSE	Multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC ...	0.05	-	nuc	0					424
P55803 UniProt NPD GO	MOG_BOVIN	Myelin-oligodendrocyte glycoprotein precursor	0.05	-	end	2	Membrane; multi-pass membrane protein				246
Q63345 UniProt NPD GO	MOG_RAT	Myelin-oligodendrocyte glycoprotein precursor	0.05	-	end	3 *	Membrane; multi-pass membrane protein			1PKQ	245
P46980 UniProt NPD GO	MY14_PHEVI	Myoactive tetradecapeptide (PTP)	0.05	-		0					14
P51537 UniProt NPD GO	MYG_NORMA	Myoglobin	0.05	-	cyt	0					377
P17724 UniProt NPD GO	GLB_TETPY	Myoglobin (Hemoglobin)	0.05	-	cyt	0					121
P17209 UniProt NPD GO	MYL4_RAT	Myosin light polypeptide 4 (Myosin light chain 1, atrial isoform)	0.05	-	cyt	0					192
O13504 UniProt NPD GO	TRPF_PICPA	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.05	-	cyt	0					237
Q01415 UniProt NPD GO	GALK2_HUMAN	N-acetylgalactosamine kinase (EC 2.7.1.157) (GalNAc kinase) (Galactokinase 2)	0.05	-	nuc	0			137028	2A2D	458
Q5R6J8 UniProt NPD GO	GALK2_PONPY	N-acetylgalactosamine kinase (EC 2.7.1.157) (GalNAc kinase) (Galactokinase 2)	0.05	-	nuc	0					458
Q9QZ08 UniProt NPD GO	NAGK_MOUSE	N-acetylglucosamine kinase (EC 2.7.1.59) (GlcNAc kinase)	0.05	-	cyt	0		soluble fraction [IDA]			342
P68827 UniProt NPD GO	NAGPA_BOVIN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (EC 3.1.4.45) (Phosphodiester alp ...	0.05	-	cyt	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type I membrane protein (By similari ...				33
Q5KTC7 UniProt NPD GO	ASAHL_RAT	N-acylethanolamine-hydrolyzing acid amidase precursor (EC 3.5.1.-) (N-acylsphingosine amidohydrolase ...	0.05	-	exc	0	Lysosome (Probable)				362
Q02083 UniProt NPD GO	ASAHL_HUMAN	N-acylethanolamine-hydrolyzing acid amidase precursor (EC 3.5.1.-) (N-acylsphingosine amidohydrolase ...	0.05	-	exc	1 *	Lysosome (Probable)	cytoplasm [IDA]	607469		359

You are viewing entries 74901 to 74950 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.