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
Q9HGZ0 UniProt NPD GO	K6PF2_ASPOR	6-phosphofructokinase subunit beta (EC 2.7.1.11) (Phosphofructokinase 2) (Phosphohexokinase) (6PF-1- ...	0.40	-	cyt	0	Cytoplasm (By similarity)				775
Q12690 UniProt NPD GO	RL13A_YEAST	60S ribosomal protein L13-A	0.40	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			199
P40212 UniProt NPD GO	RL13B_YEAST	60S ribosomal protein L13-B	0.40	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			199
P51418 UniProt NPD GO	R18A2_ARATH	60S ribosomal protein L18a-2	0.40	-	nuc	0					178
Q6BXM5 UniProt NPD GO	RL3_DEBHA	60S ribosomal protein L3	0.40	+	mit	0	Cytoplasm (By similarity)				389
P87262 UniProt NPD GO	RL34A_YEAST	60S ribosomal protein L34-A	0.40	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			121
O02056 UniProt NPD GO	RL4_CAEEL	60S ribosomal protein L4	0.40	-	cyt	0					344
P36519 UniProt NPD GO	RM07_YEAST	60S ribosomal protein L7, mitochondrial precursor (YmL7)	0.40	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			292
P35685 UniProt NPD GO	RL7A_ORYSA	60S ribosomal protein L7a	0.40	-	mit	0					258
P62425 UniProt NPD GO	RL7A_RAT	60S ribosomal protein L7a	0.40	-	nuc	0					265
P12970 UniProt NPD GO	RL7A_MOUSE	60S ribosomal protein L7a (Surfeit locus protein 3)	0.40	-	nuc	0					265
P62424 UniProt NPD GO	RL7A_HUMAN	60S ribosomal protein L7a (Surfeit locus protein 3) (PLA-X polypeptide)	0.40	-	nuc	0			185640		265
O14464 UniProt NPD GO	YP18B_YEAST	60S ribosomal protein YPL183W-A, mitochondrial precursor	0.40	-	mit	0	Mitochondrion				93
Q923W9 UniProt NPD GO	ADA33_MOUSE	ADAM 33 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 33)	0.40	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			797
Q5REU3 UniProt NPD GO	ARL4D_PONPY	ADP-ribosylation factor-like protein 4D (ADP-ribosylation factor-like protein 4L)	0.40	-	mit	0	Nucleus; nucleolus (By similarity)				201
Q9Y4X0 UniProt NPD GO	AMER1_HUMAN	AMME syndrome candidate gene 1 protein	0.40	-	nuc	0			300195		333
P27641 UniProt NPD GO	KU86_MOUSE	ATP-dependent DNA helicase 2 subunit 2 (EC 3.6.1.-) (ATP-dependent DNA helicase II 80 kDa subunit) ( ...	0.40	-	cyt	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			731
Q4P7Z8 UniProt NPD GO	DBP5_USTMA	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.40	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				456
Q59PR3 UniProt NPD GO	DBP8_CANAL	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.40	-	mit	0	Nucleus; nucleolus (By similarity)				440
Q755C5 UniProt NPD GO	MRH4_ASHGO	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-)	0.40	-	mit	0	Mitochondrion (By similarity)				554
Q2U8K6 UniProt NPD GO	DBP5_ASPOR	ATP-dependent RNA helicase dbp5 (EC 3.6.1.-)	0.40	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				487
Q2U5A2 UniProt NPD GO	DHH1_ASPOR	ATP-dependent RNA helicase dhh1 (EC 3.6.1.-)	0.40	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				511
Q6CXT4 UniProt NPD GO	IF4A_KLULA	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.40	-	cyt	0	Cytoplasm (By similarity)				396
Q7SF55 UniProt NPD GO	ACN9_NEUCR	Acetate non-utilizing protein 9, mitochondrial precursor	0.40	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				148
P11029 UniProt NPD GO	COAC_CHICK	Acetyl-CoA carboxylase (EC 6.4.1.2) (ACC) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.40	-	nuc	0	Cytoplasm				2324
Q93149 UniProt NPD GO	ACR3_CAEEL	Acetylcholine receptor subunit beta-type acr-3 precursor	0.40	-	end	5 *	Membrane; multi-pass membrane protein				487
O35167 UniProt NPD GO	COLQ_RAT	Acetylcholinesterase collagenic tail peptide precursor (AChE Q subunit) (Acetylcholinesterase-associ ...	0.40	-	nuc	0		basal lamina [TAS]			458
P49911 UniProt NPD GO	AN32A_RAT	Acidic leucine-rich nuclear phosphoprotein 32 family member A (Leucine-rich acidic nuclear protein)	0.40	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)	cytoplasm [TAS] nucleus [TAS]			247
Q92688 UniProt NPD GO	AN32B_HUMAN	Acidic leucine-rich nuclear phosphoprotein 32 family member B (PHAPI2 protein) (Silver-stainable pro ...	0.40	-	nuc	0	Nucleus. Accumulates in the nuclei at the S phase (By similarity)				251
Q4V8X4 UniProt NPD GO	ACBD6_BRARE	Acyl-CoA-binding domain-containing protein 6	0.40	-	nuc	0					300
P28645 UniProt NPD GO	STAD_SPIOL	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.40	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				399
P30804 UniProt NPD GO	ADCY6_CANFA	Adenylate cyclase type 6 (EC 4.6.1.1) (Adenylate cyclase type VI) (ATP pyrophosphate-lyase 6) (Ca(2+ ...	0.40	-	end	12	Membrane; multi-pass membrane protein				1165
P21265 UniProt NPD GO	PUR8_CHICK	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.40	-	mit	0					459
Q640T1 UniProt NPD GO	ALLC_XENTR	Allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.40	-	cyt	0					389
P02504 UniProt NPD GO	CRYAA_CHICK	Alpha crystallin A chain	0.40	-	nuc	0					173
P02506 UniProt NPD GO	CRYAA_TUPTE	Alpha crystallin A chain	0.40	-	nuc	0					173
Q8HYJ6 UniProt NPD GO	FUT6_GORGO	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.40	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
P51993 UniProt NPD GO	FUT6_HUMAN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.40	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	Golgi apparatus [TAS]	136836		359
Q13424 UniProt NPD GO	SNTA1_HUMAN	Alpha-1-syntrophin (59 kDa dystrophin-associated protein A1 acidic component 1) (Pro-TGF-alpha cytop ...	0.40	-	mit	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity). In ...		601017		505
Q61301 UniProt NPD GO	CTN2_MOUSE	Alpha-2 catenin (Alpha-catenin-related protein) (Alpha N-catenin)	0.40	-	nuc	0		cell-cell adherens junction [IDA] lamellipodium [IDA]			952
Q61247 UniProt NPD GO	A2AP_MOUSE	Alpha-2-antiplasmin precursor (Alpha-2-plasmin inhibitor) (Alpha-2-PI) (Alpha-2-AP)	0.40	-	end	0	Secreted protein				491
O77700 UniProt NPD GO	ADA2B_BOVIN	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.40	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				392
P61642 UniProt NPD GO	SIA8A_PANTR	Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase (EC 2.4.99.8) (Ganglioside GD3 synthase) (Gang ...	0.40	+	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				356
P23631 UniProt NPD GO	LATA_LATMA	Alpha-latrotoxin precursor (Alpha-LTX)	0.40	-	cyt	0	Secreted protein				1401
P19228 UniProt NPD GO	CAS1_MOUSE	Alpha-s1-casein precursor	0.40	-	exc	0	Secreted protein				313
P04724 UniProt NPD GO	GDA4_WHEAT	Alpha/beta-gliadin A-IV precursor (Prolamin)	0.40	-	nuc	0					297
P18573 UniProt NPD GO	GDA9_WHEAT	Alpha/beta-gliadin MM1 precursor (Prolamin)	0.40	-	exc	0					307
Q8X1N9 UniProt NPD GO	AOX_BLUGR	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.40	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				358
O00213 UniProt NPD GO	APBB1_HUMAN	Amyloid beta A4 precursor protein-binding family B member 1 (Fe65 protein)	0.40	-	nuc	0		growth cone [IDA] lamellipodium [IDA] nucleus [ISS] synapse [IDA]	602709		710
P26324 UniProt NPD GO	VSP1_AGKRH	Ancrod (EC 3.4.21.74) (Venombin A) (Protein C activator) (ACC-C)	0.40	-	nuc	0	Secreted protein				234

You are viewing entries 31601 to 31650 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.