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
P25100 UniProt NPD GO	ADA1D_HUMAN	Alpha-1D adrenergic receptor (Alpha 1D-adrenoceptor) (Alpha 1D-adrenoreceptor) (Alpha-1A adrenergic ...	0.29	+	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	104219		572
Q60474 UniProt NPD GO	ADA2A_CAVPO	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha-2AAR)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				450
P08913 UniProt NPD GO	ADA2A_HUMAN	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha-2AAR) (Alpha-2 ...	0.29	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	104210	1HOF	450
Q9SAC6 UniProt NPD GO	GWD1_ARATH	Alpha-glucan water dikinase 1, chloroplast precursor (EC 2.7.9.4) (Protein starch-related R1) (Prote ...	0.29	-	nuc	0	Plastid; chloroplast. Starch granules				1399
O04893 UniProt NPD GO	AGLU_SPIOL	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.29	-	exc	1 *					903
P29064 UniProt NPD GO	AGLU_CANTS	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase) [Contains: Alpha-glucosidase subunit 1; Alpha-gl ...	0.29	-	nuc	0					1070
P32602 UniProt NPD GO	SEC17_YEAST	Alpha-soluble NSF attachment protein (SNAP-alpha) (N-ethylmaleimide-sensitive factor attachment prot ...	0.29	-	nuc	0	Membrane; peripheral membrane protein	peripheral to membrane of membrane fraction [IDA]		1QQE	291
O93853 UniProt NPD GO	AOX1_CANAL	Alternative oxidase 1, mitochondrial precursor (EC 1.-.-.-)	0.29	-	mit	1	Mitochondrion (By similarity). Possibly in the inner surface of the inner mitochondrial membrane (By ...				379
Q9XSX7 UniProt NPD GO	AMBN_BOVIN	Ameloblastin precursor	0.29	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [ISS]			392
Q91ZT7 UniProt NPD GO	ASB10_MOUSE	Ankyrin repeat and SOCS box protein 10 (ASB-10)	0.29	-	cyt	0					467
Q9D738 UniProt NPD GO	ASB12_MOUSE	Ankyrin repeat and SOCS box protein 12 (ASB-12)	0.29	-	nuc	0					308
Q8BZ25 UniProt NPD GO	ANKK1_MOUSE	Ankyrin repeat and protein kinase domain-containing protein 1 (EC 2.7.11.1)	0.29	-	mit	0					745
P12429 UniProt NPD GO	ANXA3_HUMAN	Annexin A3 (Annexin III) (Lipocortin III) (Placental anticoagulant protein III) (PAP-III) (35-alpha ...	0.29	-	nuc	0		cytoplasm [TAS]	106490	1AXN	322
P51074 UniProt NPD GO	ANX4_FRAAN	Annexin-like protein RJ4	0.29	-	cyt	0					314
P49930 UniProt NPD GO	PMP23_PIG	Antibacterial peptide PMAP-23 precursor (Myeloid antibacterial peptide 23)	0.29	-	mit	1 *	Secreted protein				153
Q63191 UniProt NPD GO	AEGP_RAT	Apical endosomal glycoprotein precursor	0.29	-	end	1	Membrane; single-pass type I membrane protein (Probable)				1216
Q9TLS4 UniProt NPD GO	CYF_CYACA	Apocytochrome f precursor	0.29	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q6VU70 UniProt NPD GO	APL3_HYPCU	Apolipophorin-3 precursor (Apolipophorin-III) (ApoLp-III)	0.29	-	exc	0	Secreted protein (By similarity)				187
O14727 UniProt NPD GO	APAF_HUMAN	Apoptotic protease-activating factor 1 (Apaf-1)	0.29	-	cyt	0	Cytoplasm	cytosol [TAS]	602233	3YGS	1248
P27479 UniProt NPD GO	LOX12_BOVIN	Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) (12-LOX)	0.29	-	cyt	0	Cytoplasm				662
O15992 UniProt NPD GO	KARG_ANTJA	Arginine kinase (EC 2.7.3.3) (AK)	0.29	-	cyt	0					715
Q9HAU8 UniProt NPD GO	RNPL1_HUMAN	Arginyl aminopeptidase-like 1 (EC 3.4.11.-) (RNPEP-like protein)	0.29	-	cyt	0			605287		494
Q6BU46 UniProt NPD GO	SYNC_DEBHA	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS)	0.29	-	cyt	0	Cytoplasm (By similarity)				552
Q8BP47 UniProt NPD GO	SYNC_MOUSE	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS)	0.29	-	cyt	0	Cytoplasm				547
P16066 UniProt NPD GO	ANPRA_HUMAN	Atrial natriuretic peptide receptor A precursor (ANP-A) (ANPRA) (GC-A) (Guanylate cyclase) (EC 4.6.1 ...	0.29	-	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [IC]	108960		1061
Q755K3 UniProt NPD GO	ATG16_ASHGO	Autophagy protein 16	0.29	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				124
Q51P78 UniProt NPD GO	ATG12_MAGGR	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.29	-	mit	0	Cytoplasm (Probable)				181
Q5BCH0 UniProt NPD GO	ATG12_EMENI	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier atg12)	0.29	-	mit	0	Cytoplasm (Probable)				163
Q6BSC4 UniProt NPD GO	ATG3_DEBHA	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.29	-	mit	0	Cytoplasm (By similarity)				324
Q5KN30 UniProt NPD GO	ATG8_CRYNE	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.29	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				126
Q4WJ27 UniProt NPD GO	ATG8_ASPFU	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier atg8)	0.29	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				118
Q6K846 UniProt NPD GO	IAA9_ORYSA	Auxin-responsive protein IAA9 (Indoleacetic acid-induced protein 9)	0.29	+	cyt	0	Nucleus (By similarity)				182
Q9XFB1 UniProt NPD GO	YAB3_ARATH	Axial regulator YABBY3	0.29	-	nuc	0	Nucleus (By similarity)				240
Q86Y30 UniProt NPD GO	BAGE2_HUMAN	B melanoma antigen 2 precursor	0.29	-	end	0					109
Q86Y29 UniProt NPD GO	BAGE3_HUMAN	B melanoma antigen 3 precursor	0.29	-	exc	0					109
P33145 UniProt NPD GO	CADHK_CHICK	B-cadherin precursor (K-CAM protein) (Fragment)	0.29	-	nuc	1	Membrane; single-pass type I membrane protein				732
Q4JHS0 UniProt NPD GO	BID_PIG	BH3-interacting domain death agonist	0.29	-	cyt	0	Cytoplasm (By similarity)				192
Q9CWU6 UniProt NPD GO	BZFB_MOUSE	Basic FGF-repressed Zic-binding protein (mbFZb)	0.29	-	mit	0	Cytoplasmic vesicle (Probable). Cytoplasmic vesicular structures (Probable)	cytoplasmic membrane-bound vesicle [IDA]			295
P59017 UniProt NPD GO	B2L13_MOUSE	Bcl-2-like 13 protein (Protein Mil1) (Bcl-rambo)	0.29	-	nuc	1	Mitochondrion (By similarity)	integral to membrane [ISS] mitochondrion [ISS]			434
Q91ZE9 UniProt NPD GO	BMF_MOUSE	Bcl-2-modifying factor	0.29	-	nuc	0		cytoplasm [IDA] myosin [IDA]			185
Q8NFU0 UniProt NPD GO	VMDL2_HUMAN	Bestrophin-3 (Vitelliform macular dystrophy 2-like protein 2)	0.29	-	cyt	2 *	Cell membrane; multi-pass membrane protein	integral to membrane [IC]	607336		473
P49152 UniProt NPD GO	CRBA4_CHICK	Beta crystallin A4	0.29	-	mit	0					196
P47899 UniProt NPD GO	ADRB1_MACMU	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.29	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				480
O12971 UniProt NPD GO	LFNG_CHICK	Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.29	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				363
Q30KQ9 UniProt NPD GO	DB111_HUMAN	Beta-defensin 111 precursor (Defensin, beta 111) (Beta-defensin 11) (DEFB-11)	0.29	-	mit	0	Secreted protein (By similarity)				67
P49235 UniProt NPD GO	BGLC_MAIZE	Beta-glucosidase, chloroplast precursor (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside g ...	0.29	-	nuc	0	Plastid; chloroplast			1V08	566
O08524 UniProt NPD GO	TECTB_MOUSE	Beta-tectorin precursor	0.29	-	end	0	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Found in the non-collagenous ...	extracellular matrix (sensu Metazoa) [IDA]			329
O43252 UniProt NPD GO	PAPS1_HUMAN	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfu ...	0.29	-	cyt	0		intracellular [ISS]	603262	1XNJ	624
Q60967 UniProt NPD GO	PAPS1_MOUSE	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfu ...	0.29	-	cyt	0		intracellular [ISS] sulfate adenylyltransferase complex (ATP) [IC]			624
Q10663 UniProt NPD GO	GCP_CAEEL	Bifunctional glyoxylate cycle protein (GEX-interacting protein 7) [Includes: Isocitrate lyase (EC 4. ...	0.29	-	cyt	0					968

You are viewing entries 41001 to 41050 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.