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
Q9R0Y5 UniProt NPD GO	KAD1_MOUSE	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.09	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] mitochondrion [IDA] plasma membrane [IDA]			194
P00257 UniProt NPD GO	ADX_BOVIN	Adrenodoxin, mitochondrial precursor (Adrenal ferredoxin) (Ferredoxin-1) (Hepato-ferredoxin)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]		2BT6	186
O43488 UniProt NPD GO	ARK72_HUMAN	Aflatoxin B1 aldehyde reductase member 2 (EC 1.-.-.-) (AFB1-AR 1) (Aldoketoreductase 7)	0.09	-	mit	0	Golgi apparatus (By similarity)		603418	2BP1	359
Q8NHP1 UniProt NPD GO	ARK74_HUMAN	Aflatoxin B1 aldehyde reductase member 4 (EC 1.-.-.-) (Fragment)	0.09	-	cyt	0					319
P18676 UniProt NPD GO	LECB2_MACPO	Agglutinin beta-2 chain (MPA)	0.09	-		0				1JOT	20
P81112 UniProt NPD GO	ABA2_TRIAB	Alboaggregin-A subunit 2	0.09	-	cyt	0	Secreted protein				134
Q8VC28 UniProt NPD GO	AK1CD_MOUSE	Aldo-keto reductase family 1 member C13 (EC 1.1.1.-)	0.09	-	cyt	0					323
P52895 UniProt NPD GO	AK1C2_HUMAN	Aldo-keto reductase family 1 member C2 (EC 1.-.-.-) (Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase ...	0.09	-	cyt	0	Cytoplasm (Potential)		600450	1XJB	323
Q9GKX6 UniProt NPD GO	GALM_PIG	Aldose 1-epimerase (EC 5.1.3.3) (Galactose mutarotase)	0.09	-	cyt	0	Cytoplasm (Probable)				342
O60109 UniProt NPD GO	PPB_SCHPO	Alkaline phosphatase (EC 3.1.3.1)	0.09	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				532
P15365 UniProt NPD GO	DAL5_YEAST	Allantoate permease	0.09	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IMP]			543
P39674 UniProt NPD GO	MAG29_DERFA	Allergen MAG29 (Fragment)	0.09	-	cyt	0					145
Q9TLS8 UniProt NPD GO	PHAB_CYACA	Allophycocyanin beta chain	0.09	-	cyt	0	Plastid; chloroplast				161
P0C147 UniProt NPD GO	ALG10_MAGGR	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.09	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				660
Q6C3V7 UniProt NPD GO	ALG2_YARLI	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.09	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				460
Q96WW6 UniProt NPD GO	ALG2_SCHPO	Alpha-1,3-mannosyltransferase alg2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.09	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				511
Q8RU27 UniProt NPD GO	UPTG2_SOLTU	Alpha-1,4-glucan-protein synthase [UDP-forming] 2 (EC 2.4.1.112) (UDP-glucose:protein transglucosyla ...	0.09	-	cyt	0	Cell wall (By similarity). Cell wall; cell-cell junction; plasmodesma (By similarity). Cell wall-ass ...				366
P21350 UniProt NPD GO	A1AG1_MUSCR	Alpha-1-acid glycoprotein 1 precursor (AGP 1) (Orosomucoid-1) (OMD 1)	0.09	-	exc	0	Secreted protein				207
O54758 UniProt NPD GO	ALMS_TAMSI	Alpha-1-antitrypsin-like protein CM55-MS precursor	0.09	-	end	0	Secreted protein (By similarity)				413
P58782 UniProt NPD GO	CXVA_CONER	Alpha-A-conotoxin EIVA	0.09	-	nuc	0	Secreted protein			1PQR	30
P42255 UniProt NPD GO	ABFB_ASPNG	Alpha-N-arabinofuranosidase B precursor (EC 3.2.1.55) (Arabinosidase B) (ABF B)	0.09	-	exc	0					499
Q99K67 UniProt NPD GO	AASS_MOUSE	Alpha-aminoadipic semialdehyde synthase, mitochondrial precursor (LKR/SDH) [Includes: Lysine ketoglu ...	0.09	-	mit	0	Mitochondrion	mitochondrion [TAS]			926
P56636 UniProt NPD GO	CXA2_CONMA	Alpha-conotoxin MII precursor (CtxMII) (M2) (Fragment)	0.09	-	nuc	0	Secreted protein			2AK0	41
Q42656 UniProt NPD GO	AGAL_COFAR	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase)	0.09	-	cyt	0					378
P08896 UniProt NPD GO	LALB2_HORSE	Alpha-lactalbumin B/C (Lactose synthase B protein)	0.09	-	mit	0	Secreted protein				123
Q9YGJ5 UniProt NPD GO	NXSA2_NAJSP	Alpha-neurotoxin NTX-2 precursor	0.09	-	nuc	0	Secreted protein				83
O57327 UniProt NPD GO	NXSA4_NAJSP	Alpha-neurotoxin NTX-4 precursor	0.09	-	nuc	0	Secreted protein				83
O35403 UniProt NPD GO	ST3A1_MOUSE	Amine sulfotransferase (EC 2.8.2.3) (Sulfotransferase 3A1) (SULT-X2)	0.09	-	cyt	0	Cytoplasm (By similarity)				293
P40260 UniProt NPD GO	MEP1_YEAST	Ammonium transporter MEP1	0.09	-	end	11 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]			492
P19707 UniProt NPD GO	SAA_FELCA	Amyloid protein A (Amyloid fibril protein AA)	0.09	-	cyt	0					90
Q16937 UniProt NPD GO	ASP_ANCCA	Ancylostoma secreted protein precursor	0.09	-	exc	0	Secreted protein (Potential)				424
Q8VHS6 UniProt NPD GO	ASB15_MOUSE	Ankyrin repeat and SOCS box protein 15 (ASB-15)	0.09	-	cyt	0					583
Q8N9B4 UniProt NPD GO	ANR42_HUMAN	Ankyrin repeat domain-containing protein 42	0.09	-	cyt	0					389
Q2QLH1 UniProt NPD GO	ASZ1_OTOGA	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.09	-	nuc	0	Cytoplasm (By similarity)				475
Q9NFS4 UniProt NPD GO	ANXE2_GIALA	Annexin E1 (Annexin XXI)	0.09	-	cyt	0	Flagellum				337
P24773 UniProt NPD GO	TRPG_PENCH	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.09	-	nuc	0					752
O19914 UniProt NPD GO	TRPG_CYACA	Anthranilate synthase component II (EC 4.1.3.27) (Glutamine amido-transferase)	0.09	-	cyt	0	Plastid; chloroplast				195
Q6DFX2 UniProt NPD GO	ANTR2_MOUSE	Anthrax toxin receptor 2 precursor	0.09	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)				487
P80393 UniProt NPD GO	AMP3_MELGA	Antimicrobial peptide THP3 (Turkey heterophil peptide 3) (Fragment)	0.09	-	nuc	0	Secreted protein				25
P84528 UniProt NPD GO	RNAM_PLESA	Antimicrobial ribonuclease (EC 3.1.-.-) (Fragment)	0.09	-		0					10
P24477 UniProt NPD GO	RIP2_DIACA	Antiviral protein DAP-32 (EC 3.2.2.22) (Ribosome-inactivating protein) (rRNA N-glycosidase) (Fragmen ...	0.09	-	nuc	0					60
Q02793 UniProt NPD GO	SKI8_YEAST	Antiviral protein SKI8	0.09	-	cyt	0		cytoplasm [IPI] nuclear chromosome [IDA]		1SQ9	397
Q85FK9 UniProt NPD GO	CYF_ADICA	Apocytochrome f precursor	0.09	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				321
P36438 UniProt NPD GO	CYF_BRARA	Apocytochrome f precursor	0.09	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein			2PCF	320
O78494 UniProt NPD GO	CYF_GUITH	Apocytochrome f precursor	0.09	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				321
Q9TKZ1 UniProt NPD GO	CYF_NEPOL	Apocytochrome f precursor	0.09	-	end	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				313
P05151 UniProt NPD GO	CYF_WHEAT	Apocytochrome f precursor	0.09	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P12278 UniProt NPD GO	APOC2_CANFA	Apolipoprotein C-II precursor (Apo-CII) (ApoC-II)	0.09	-	exc	0	Secreted protein				101
Q07814 UniProt NPD GO	BAXB_HUMAN	Apoptosis regulator BAX, cytoplasmic isoform beta	0.09	-	nuc	0	Cytoplasm		600040		218
Q6BEG6 UniProt NPD GO	GHRL_FELCA	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.09	-	vac	0	Secreted protein				117

You are viewing entries 65701 to 65750 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.