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
Q60Q90 UniProt NPD GO	PUR8_CAEBR	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.30	-	cyt	0					478
P46590 UniProt NPD GO	ALS1_CANAL	Agglutinin-like protein 1 precursor	0.30	-	nuc	0					1260
P25409 UniProt NPD GO	ALAT1_RAT	Alanine aminotransferase 1 (EC 2.6.1.2) (ALT1) (Glutamic--pyruvic transaminase 1) (GPT 1) (Glutamic- ...	0.30	-	cyt	0	Cytoplasm				495
Q6NS38 UniProt NPD GO	ALKB2_HUMAN	Alkylated repair protein alkB homolog 2 (Oxy DC1)	0.30	-	cyt	0					261
P02474 UniProt NPD GO	CRYAA_BALAC	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.30	-	mit	0					173
P02484 UniProt NPD GO	CRYAA_MANJA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.30	-	nuc	0					173
P02483 UniProt NPD GO	CRYAA_MUSVI	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.30	-	cyt	0					173
P02492 UniProt NPD GO	CRYAA_OCHPR	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.30	-	mit	0					173
P82530 UniProt NPD GO	CRYAA_ELERU	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form] (Fragments)	0.30	-	cyt	0					161
Q11128 UniProt NPD GO	FUT5_HUMAN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.30	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	Golgi apparatus [TAS]	136835		374
Q9BYC5 UniProt NPD GO	FUT8_HUMAN	Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) (Glycoprotein 6-alpha-L-fucosyltransferase) (GDP-fucose ...	0.30	+	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...	Golgi apparatus [NAS]	602589		575
Q6EV77 UniProt NPD GO	FUT8_PANTR	Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) (Glycoprotein 6-alpha-L-fucosyltransferase) (GDP-fucose ...	0.30	+	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				575
P27808 UniProt NPD GO	MGAT1_MOUSE	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) (N-glycosyl-ol ...	0.30	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				447
P53536 UniProt NPD GO	PHSL_VICFA	Alpha-1,4 glucan phosphorylase L isozyme, chloroplast precursor (EC 2.4.1.1) (Starch phosphorylase L ...	0.30	-	nuc	0	Plastid; chloroplast. Plastid; amyloplast				1003
Q60590 UniProt NPD GO	A1AG1_MOUSE	Alpha-1-acid glycoprotein 1 precursor (AGP 1) (Orosomucoid-1) (OMD 1)	0.30	-	exc	0					207
Q5R536 UniProt NPD GO	AACT_PONPY	Alpha-1-antichymotrypsin precursor (ACT)	0.30	-	end	0	Secreted protein (By similarity)				423
Q00898 UniProt NPD GO	A1AT5_MOUSE	Alpha-1-antitrypsin 1-5 precursor (Serine protease inhibitor 1-5) (Alpha-1 protease inhibitor 5)	0.30	-	end	0	Secreted protein				413
P14046 UniProt NPD GO	A1I3_RAT	Alpha-1-inhibitor 3 precursor (Alpha-1-inhibitor III)	0.30	-	cyt	1 *	Secreted protein				1477
Q28626 UniProt NPD GO	SNTA1_RABIT	Alpha-1-syntrophin (59 kDa dystrophin-associated protein A1 acidic component 1) (59-1 DAP) (Syntroph ...	0.30	-	cyt	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity). In ...				505
O02666 UniProt NPD GO	ADA1D_RABIT	Alpha-1D adrenergic receptor (Alpha 1D-adrenoceptor) (Alpha 1D-adrenoreceptor)	0.30	+	end	7	Membrane; multi-pass membrane protein				576
O19014 UniProt NPD GO	ADA2B_ELEMA	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.30	-	end	6 *	Membrane; multi-pass membrane protein				384
P02663 UniProt NPD GO	CAS2_BOVIN	Alpha-S2-casein precursor [Contains: Casocidin-1 (Casocidin-I)]	0.30	-	exc	0	Secreted protein				222
P09115 UniProt NPD GO	CAS1_RABIT	Alpha-casein precursor (Alpha-S1-casein)	0.30	-	mit	0	Secreted protein				215
Q8BWP5 UniProt NPD GO	TTPA_MOUSE	Alpha-tocopherol transfer protein (Alpha-TTP)	0.30	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]			278
Q8NJ59 UniProt NPD GO	AOX_BOTCI	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.30	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				361
Q80ZD9 UniProt NPD GO	AMGO2_MOUSE	Amphoterin-induced protein 2 precursor (AMIGO-2) (Alivin-1)	0.30	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Nucleus (By similarity). Associa ...	integral to plasma membrane [ISS]			519
Q8WN65 UniProt NPD GO	ANGI_MIOTA	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.30	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q8WN67 UniProt NPD GO	ANGI_PONPY	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.30	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			147
Q861Y1 UniProt NPD GO	ANGI_PYGAV	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.30	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q861Y2 UniProt NPD GO	ANGI_PYGBI	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.30	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q861Y3 UniProt NPD GO	ANGI_PYGRO	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.30	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q96Q27 UniProt NPD GO	ASB2_HUMAN	Ankyrin repeat and SOCS box protein 2 (ASB-2)	0.30	-	mit	0			605759		587
Q9NXR5 UniProt NPD GO	ANR10_HUMAN	Ankyrin repeat domain-containing protein 10	0.30	-	nuc	0					420
Q53RE8 UniProt NPD GO	ANR39_HUMAN	Ankyrin repeat domain-containing protein 39	0.30	+	nuc	0					183
Q8WMX6 UniProt NPD GO	ASZ1_PANTR	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.30	-	nuc	0	Cytoplasm (By similarity)				475
O35639 UniProt NPD GO	ANXA3_MOUSE	Annexin A3 (Annexin III) (Lipocortin III) (Placental anticoagulant protein III) (PAP-III) (35-alpha ...	0.30	-	cyt	0					322
P13928 UniProt NPD GO	ANXA8_HUMAN	Annexin A8 (Annexin VIII) (Vascular anticoagulant-beta) (VAC-beta)	0.30	-	cyt	0			602396	1W45	327
P26256 UniProt NPD GO	ANX12_HYDAT	Annexin-B12 (Annexin-12) (Annexin XII)	0.30	-	mit	0				1DM5	316
P49932 UniProt NPD GO	PMP37_PIG	Antibacterial peptide PMAP-37 precursor (Myeloid antibacterial peptide 37)	0.30	-	mit	1 *	Secreted protein				167
Q07839 UniProt NPD GO	EG13_ECHGR	Antigen EG13	0.30	-	nuc	0					416
Q41258 UniProt NPD GO	AMP1_ALLCE	Antimicrobial protein Ace-AMP1 precursor	0.30	-	mit	1 *					132
Q9WV08 UniProt NPD GO	APJ_MOUSE	Apelin receptor (G-protein coupled receptor APJ) (Angiotensin receptor-like 1) (MSR)	0.30	+	end	7 *	Membrane; multi-pass membrane protein				377
P16445 UniProt NPD GO	AMA1_PLACH	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.30	-	cyt	1	Membrane; single-pass type I membrane protein				558
P32918 UniProt NPD GO	APOA1_COTJA	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.30	-	exc	0	Secreted protein				264
O15296 UniProt NPD GO	LX15B_HUMAN	Arachidonate 15-lipoxygenase type II (EC 1.13.11.33) (15-LOX-2) (15-lipoxygenase 2)	0.30	-	cyt	0	Cytoplasm (By similarity)	intracellular [IDA]	603697		676
Q95MP0 UniProt NPD GO	AIPL1_MACMU	Aryl-hydrocarbon-interacting protein-like 1	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				392
P13914 UniProt NPD GO	ARY2_CHICK	Arylamine N-acetyltransferase, pineal gland isozyme NAT-3 (EC 2.3.1.5) (Arylamine acetylase)	0.30	-	cyt	0					290
P33727 UniProt NPD GO	ARSB_FELCA	Arylsulfatase B precursor (EC 3.1.6.12) (ASB) (N-acetylgalactosamine-4-sulfatase) (G4S)	0.30	-	mit	0	Lysosome				535
P34927 UniProt NPD GO	ASGR1_MOUSE	Asialoglycoprotein receptor 1 (ASGPR 1) (ASGP-R 1) (Hepatic lectin 1) (MHL-1)	0.30	-	nuc	1 *	Membrane; single-pass type II membrane protein				283
Q5K6S9 UniProt NPD GO	ATG5_CRYNE	Autophagy protein 5	0.30	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				339

You are viewing entries 40101 to 40150 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.