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
P16000 UniProt NPD GO	ATP9_EMENI	ATP synthase protein 9, mitochondrial precursor (EC 3.6.3.14) (Lipid-binding protein)	0.18	-	end	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				143
Q85FN4 UniProt NPD GO	ATPA_ADICA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q85AU2 UniProt NPD GO	ATPA_ANTFO	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P35009 UniProt NPD GO	ATPA_GALSU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				505
Q85X67 UniProt NPD GO	ATPA_PINKO	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				494
P06450 UniProt NPD GO	ATPA_SPIOL	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)			1KMH	507
Q9XXK1 UniProt NPD GO	ATPA_CAEEL	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.18	-	mit	0	Mitochondrion; mitochondrial inner membrane				538
P49375 UniProt NPD GO	ATPA_KLULA	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.18	-	mit	0	Mitochondrion				548
P56317 UniProt NPD GO	CLPP_CHLVU	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.18	-	cyt	0	Plastid; chloroplast				201
P35560 UniProt NPD GO	IRK1_RAT	ATP-sensitive inward rectifier potassium channel 1 (Potassium channel, inwardly rectifying subfamily ...	0.18	+	end	2	Membrane; multi-pass membrane protein				391
O88335 UniProt NPD GO	IRK1_MOUSE	ATP-sensitive inward rectifier potassium channel 1 (Potassium channel, inwardly rectifying subfamily ...	0.18	+	mit	2	Membrane; multi-pass membrane protein				372
Q9UII2 UniProt NPD GO	ATIF1_HUMAN	ATPase inhibitor, mitochondrial precursor	0.18	-	mit	0	Mitochondrion	mitochondrion [TAS]			106
Q5RFJ9 UniProt NPD GO	ATIF1_PONPY	ATPase inhibitor, mitochondrial precursor	0.18	-	mit	0	Mitochondrion (By similarity)				106
P17597 UniProt NPD GO	ILVB_ARATH	Acetolactate synthase, chloroplast precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase) (ALS)	0.18	-	mit	0	Plastid; chloroplast			1Z8N	670
P09691 UniProt NPD GO	ACHD_ELEEL	Acetylcholine receptor protein subunit delta (Fragment)	0.18	-	nuc	0	Membrane; multi-pass membrane protein				26
P25681 UniProt NPD GO	TXAC_DENPO	Acetylcholinesterase toxin C	0.18	-	nuc	0	Secreted protein				61
P10323 UniProt NPD GO	ACRO_HUMAN	Acrosin precursor (EC 3.4.21.10) [Contains: Acrosin light chain; Acrosin heavy chain]	0.18	-	nuc	0		acrosomal matrix [TAS]	102480		421
P18602 UniProt NPD GO	ACT3_ARTSX	Actin, clone 302 (Fragment)	0.18	-	cyt	0	Cytoplasm				327
P46680 UniProt NPD GO	AIP1_YEAST	Actin-interacting protein 1	0.18	-	cyt	0		actin cortical patch [IDA] cytoplasm [IDA] nucleus [IDA]		1PI6	615
Q09443 UniProt NPD GO	ARP6_CAEEL	Actin-like protein C08B11.6	0.18	-	cyt	0					418
Q28041 UniProt NPD GO	ACVR1_BOVIN	Activin receptor type-1 precursor (EC 2.7.11.30) (Activin receptor type I) (ACTR-I) (Serine/threonin ...	0.18	-	end	1	Membrane; single-pass type I membrane protein	activin receptor complex [ISS]			509
P80201 UniProt NPD GO	ACVR1_RAT	Activin receptor type-1 precursor (EC 2.7.11.30) (Activin receptor type I) (ACTR-I) (Serine/threonin ...	0.18	-	end	1	Membrane; single-pass type I membrane protein	activin receptor complex [IDA]			509
Q9UKU7 UniProt NPD GO	ACAD8_HUMAN	Acyl-CoA dehydrogenase family member 8, mitochondrial precursor (EC 1.3.99.-) (ACAD-8) (Isobutyryl-C ...	0.18	-	mit	0	Mitochondrion		604773	1RX0	415
P13711 UniProt NPD GO	ACOX_YEAST	Acyl-coenzyme A oxidase (EC 1.3.3.6) (Acyl-CoA oxidase)	0.18	-	mit	0	Peroxisome				748
O74935 UniProt NPD GO	ACOX2_YARLI	Acyl-coenzyme A oxidase 2 (EC 1.3.3.6) (Acyl-CoA oxidase 2)	0.18	-	cyt	0	Peroxisome				700
Q9NVZ3 UniProt NPD GO	NECP2_HUMAN	Adaptin ear-binding coat-associated protein 2 (NECAP-2)	0.18	-	cyt	0	Membrane-associated; membranes of clathrin-coated vesicles. Colocalizes with AP-2 at the plasma memb ...	clathrin vesicle coat [ISS] coated pit [ISS]			263
P49983 UniProt NPD GO	KADH_TRIVA	Adenylate kinase precursor (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK)	0.18	-	nuc	0	Hydrogenosome				229
P30520 UniProt NPD GO	PURA2_HUMAN	Adenylosuccinate synthetase isozyme 2 (EC 6.3.4.4) (Adenylosuccinate synthetase, acidic isozyme) (IM ...	0.18	-	cyt	0	Cytoplasm. Partially associated with particulate fractions		103060		456
O49196 UniProt NPD GO	KAP2_ARATH	Adenylyl-sulfate kinase 2, chloroplast precursor (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulf ...	0.18	-	nuc	0	Plastid; chloroplast (By similarity)				293
Q868F8 UniProt NPD GO	ALLS_SPOFR	Allatostatin precursor (Spofr-AS) (AS)	0.18	-	exc	1 *	Secreted protein				125
O12995 UniProt NPD GO	CRYAB_TURME	Alpha crystallin B chain (Alpha(B)-crystallin) (Fragment)	0.18	-	mit	0					52
Q9Y231 UniProt NPD GO	FUT9_HUMAN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.18	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...	Golgi apparatus [TAS]	606865		359
Q659L0 UniProt NPD GO	FUT9_PANTR	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.18	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
Q9C8W3 UniProt NPD GO	FUT13_ARATH	Alpha-(1,4)-fucosyltransferase (EC 2.4.1.-) (FT4-M) (Galactoside 3(4)-L-fucosyltransferase) (FucTC) ...	0.18	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				401
Q10254 UniProt NPD GO	ALG10_SCHPO	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.18	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				445
P53059 UniProt NPD GO	MNT2_YEAST	Alpha-1,3-mannosyltransferase MNT2 (EC 2.4.1.-)	0.18	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				558
P25227 UniProt NPD GO	A1AG_RABIT	Alpha-1-acid glycoprotein precursor (Orosomucoid) (OMD)	0.18	-	end	0					201
O15466 UniProt NPD GO	SIA8E_HUMAN	Alpha-2,8-sialyltransferase 8E (EC 2.4.99.-) (ST8Sia V)	0.18	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)		607162		376
P61646 UniProt NPD GO	SIA8E_PANTR	Alpha-2,8-sialyltransferase 8E (EC 2.4.99.-) (ST8Sia V)	0.18	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				376
Q92184 UniProt NPD GO	SIA7B_CHICK	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.18	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				404
P39036 UniProt NPD GO	CAS2_PIG	Alpha-S2-casein precursor	0.18	-	exc	0	Secreted protein				235
P21567 UniProt NPD GO	AMY1_SACFI	Alpha-amylase precursor (EC 3.2.1.1)	0.18	-	exc	0					494
P55926 UniProt NPD GO	ACCN2_RAT	Amiloride-sensitive cation channel 2, neuronal (Acid-sensing ion channel 1) (ASIC1) (Brain sodium ch ...	0.18	-	mit	0	Cell membrane; multi-pass membrane protein (By similarity). Localizes in synaptosomes at dendritic s ...				526
Q9W754 UniProt NPD GO	SCNNB_RANCA	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.18	-	cyt	0	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				273
P21396 UniProt NPD GO	AOFA_RAT	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.18	-	cyt	0	Mitochondrion; mitochondrial outer membrane			1O5W	526
Q01356 UniProt NPD GO	ARG13_NEUCR	Amino acid transporter arg-13	0.18	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				363
Q80ZD7 UniProt NPD GO	AMGO1_RAT	Amphoterin-induced protein 1 precursor (AMIGO-1) (Alivin-2)	0.18	-	end	2 *	Membrane; single-pass type I membrane protein (Potential). Associated with axons of neuronal cells	integral to plasma membrane [NAS]			493
Q12157 UniProt NPD GO	APC11_YEAST	Anaphase-promoting complex subunit 11 (EC 6.3.2.-)	0.18	-	cyt	0		anaphase-promoting complex [TAS]			165
Q8WN61 UniProt NPD GO	ANGI_AOTTR	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.18	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q8WN60 UniProt NPD GO	ANGI_SAISC	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.18	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146

You are viewing entries 52701 to 52750 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.