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
Q9R0X2 UniProt NPD GO	ADEC1_MOUSE	ADAM DEC1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain-like protein decysin 1 ...	0.74	-	nuc	0	Secreted protein				467
P97857 UniProt NPD GO	ATS1_MOUSE	ADAMTS-1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 1) ...	0.74	+	nuc	0	Secreted protein; extracellular space; extracellular matrix	basement membrane [IDA] cytoplasmic vesicle [IDA] extracellular matrix [IDA]			968
P39993 UniProt NPD GO	GEA2_YEAST	ARF guanine-nucleotide exchange factor 2	0.74	-	nuc	0	Cytoplasm; cytosol. Membrane; peripheral membrane protein. Soluble and partially membrane-bound	Golgi cis cisterna [IDA] Golgi-associated vesicle [TAS]		1KU1	1459
Q5T9A4 UniProt NPD GO	ATD3B_HUMAN	ATPase family AAA domain-containing protein 3B	0.74	-	nuc	0					648
O02767 UniProt NPD GO	ACOX2_RABIT	Acyl-coenzyme A oxidase 2, peroxisomal (EC 1.17.99.3) (3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-ch ...	0.74	-	nuc	0	Peroxisome (By similarity)				681
P43237 UniProt NPD GO	ALL11_ARAHY	Allergen Ara h 1, clone P17 precursor (Ara h I)	0.74	-	mit	0					614
Q7PKQ5 UniProt NPD GO	ACTN_ANOGA	Alpha-actinin, sarcomeric (F-actin cross linking protein)	0.74	-	cyt	0					922
P27940 UniProt NPD GO	AMYC1_ORYSA	Alpha-amylase isozyme C (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Isozyme 1B)	0.74	-	nuc	0					348
Q61180 UniProt NPD GO	SCNNA_MOUSE	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.74	-	nuc	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...	integral to membrane [IDA]			699
Q02410 UniProt NPD GO	APBA1_HUMAN	Amyloid beta A4 precursor protein-binding family A member 1 (Neuron-specific X11 protein) (Neuronal ...	0.74	-	nuc	0		synaptic vesicle [TAS]	602414	1Y7N	837
Q8K371 UniProt NPD GO	AMOL2_MOUSE	Angiomotin-like protein 2	0.74	+	nuc	0		tight junction [IDA]			772
Q8BX02 UniProt NPD GO	ANR25_MOUSE	Ankyrin repeat domain-containing protein 25	0.74	-	nuc	0					843
P98203 UniProt NPD GO	ARVC_MOUSE	Armadillo repeat protein deleted in velo-cardio-facial syndrome homolog	0.74	-	nuc	0		cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			962
P01360 UniProt NPD GO	ELHA_APLCA	Atrial gland peptide A precursor (ELH-18) [Contains: Atrial gland peptide A; Califin-A; Califin-A la ...	0.74	-	exc	0	Secreted protein				173
Q6CVG9 UniProt NPD GO	ATG11_KLULA	Autophagy-related protein 11	0.74	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1046
Q12527 UniProt NPD GO	ATG11_YEAST	Autophagy-related protein 11 (Cytoplasm to vacuole targeting protein 9)	0.74	-	nuc	0	Membrane; peripheral membrane protein. Punctate structures	extrinsic to membrane [IDA]			1178
Q6CWK2 UniProt NPD GO	ATG13_KLULA	Autophagy-related protein 13	0.74	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				684
Q5AVG2 UniProt NPD GO	ATG3_EMENI	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme atg3)	0.74	-	mit	0	Cytoplasm (By similarity)				787
Q9ZPY6 UniProt NPD GO	ARFK_ARATH	Auxin response factor 11	0.74	+	nuc	0	Nucleus				601
P93024 UniProt NPD GO	ARFE_ARATH	Auxin response factor 5 (Transcription factor MONOPTEROS) (Auxin-responsive protein IAA24)	0.74	-	nuc	0	Nucleus				902
O15169 UniProt NPD GO	AXN1_HUMAN	Axin-1 (Axis inhibition protein 1) (hAxin)	0.74	-	nuc	0	Cytoplasm	cytoplasm [NAS] lateral plasma membrane [IDA] nucleus [IDA]	114550	1EMU	862
O70240 UniProt NPD GO	AXN2_RAT	Axin-2 (Axis inhibition protein 2) (Conductin) (Axin-like protein) (Axil)	0.74	-	nuc	0	Cytoplasm				838
Q80TT2 UniProt NPD GO	BAIP3_MOUSE	BAI1-associated protein 3 (BAP3)	0.74	-	cyt	0					1134
Q9NR09 UniProt NPD GO	BIRC6_HUMAN	Baculoviral IAP repeat-containing protein 6 (Ubiquitin-conjugating BIR-domain enzyme apollon)	0.74	-	end	0			605638		4829
P08724 UniProt NPD GO	BAR1_CHIPA	Balbiani ring protein 1 (Giant secretory protein I-A) (GSP-IA) (Fragment)	0.74	+	nuc	0	Secreted protein				326
Q9NY43 UniProt NPD GO	BARH2_HUMAN	BarH-like 2 homeobox protein	0.74	+	nuc	0	Nucleus (Probable)		605212		387
Q9M7D1 UniProt NPD GO	TPSD8_ABIGR	Beta-phellandrene synthase, chloroplast precursor (EC 4.2.3.-) ((-)-(4S)-beta-phellandrene synthase) ...	0.74	-	mit	0	Plastid; chloroplast (By similarity)				630
Q3UHD1 UniProt NPD GO	BAI1_MOUSE	Brain-specific angiogenesis inhibitor 1 precursor	0.74	-	end	7 *	Cell membrane; multi-pass membrane protein. Likely to be concentrated at cell-cell adhesion sites (B ...				1582
O60241 UniProt NPD GO	BAI2_HUMAN	Brain-specific angiogenesis inhibitor 2 precursor	0.74	-	end	8	Membrane; multi-pass membrane protein	integral to membrane [TAS]	602683		1572
Q6RFL5 UniProt NPD GO	BSH_CHICK	Brain-specific homeobox protein homolog	0.74	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			233
P04003 UniProt NPD GO	C4BP_HUMAN	C4b-binding protein alpha chain precursor (C4bp) (Proline-rich protein) (PRP)	0.74	-	nuc	0		extracellular region [NAS]	120830	2A55	597
O59961 UniProt NPD GO	PT494_SACBA	COX3 mRNA-specific translational activator PET494	0.74	-	mit	1	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				489
Q6RET6 UniProt NPD GO	CCAMK_PEA	Calcium and calcium/calmodulin-dependent serine/threonine-protein kinase (EC 2.7.11.17) (PsCCaMK) (P ...	0.74	+	nuc	0					527
Q86UW7 UniProt NPD GO	CAPS2_HUMAN	Calcium-dependent secretion activator 2 (Calcium-dependent activator protein for secretion 2) (CAPS- ...	0.74	-	nuc	0	Cytoplasmic vesicle. Membrane-associated to vesicles. Strongly enriched in synaptic fractions. Proba ...		609978		1296
Q14123 UniProt NPD GO	PDE1C_HUMAN	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C (EC 3.1.4.17) (Cam-PDE 1C) ...	0.74	+	nuc	0			602987	1LXS	709
Q07250 UniProt NPD GO	KCCS_MALDO	Calcium/calmodulin-dependent serine/threonine-protein kinase (EC 2.7.11.17)	0.74	+	nuc	0					415
Q92177 UniProt NPD GO	CAN3_CHICK	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.74	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				810
Q9NPF2 UniProt NPD GO	CHSTB_HUMAN	Carbohydrate sulfotransferase 11 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 1) (Chondroitin 4-su ...	0.74	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [NAS]			352
P39962 UniProt NPD GO	KC13_YEAST	Casein kinase I homolog 3 (EC 2.7.11.1)	0.74	-	nuc	0	Cell membrane; lipid-anchor. Nucleus	nucleus [IDA] plasma membrane [IDA] vacuolar membrane (sensu Fungi) [IDA]			524
Q14790 UniProt NPD GO	CASP8_HUMAN	Caspase-8 precursor (EC 3.4.22.-) (CASP-8) (ICE-like apoptotic protease 5) (MORT1-associated CED-3 h ...	0.74	-	nuc	0	Cytoplasm	cytoskeleton [TAS] mitochondrion [TAS]	601763	2FUN	479
Q6WBX8 UniProt NPD GO	RAD9B_HUMAN	Cell cycle checkpoint control protein RAD9B homolog (RAD9 homolog B) (hRAD9B)	0.74	-	nuc	0			608368		414
P13481 UniProt NPD GO	P53_CERAE	Cellular tumor antigen p53 (Tumor suppressor p53)	0.74	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			393
P41685 UniProt NPD GO	P53_FELCA	Cellular tumor antigen p53 (Tumor suppressor p53)	0.74	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			386
P56423 UniProt NPD GO	P53_MACFA	Cellular tumor antigen p53 (Tumor suppressor p53)	0.74	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			393
P61260 UniProt NPD GO	P53_MACFU	Cellular tumor antigen p53 (Tumor suppressor p53)	0.74	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			393
P56424 UniProt NPD GO	P53_MACMU	Cellular tumor antigen p53 (Tumor suppressor p53)	0.74	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			393
Q95330 UniProt NPD GO	P53_RABIT	Cellular tumor antigen p53 (Tumor suppressor p53)	0.74	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			391
Q15027 UniProt NPD GO	CENB1_HUMAN	Centaurin-beta 1 (Cnt-b1)	0.74	-	cyt	0			607763		740
P35203 UniProt NPD GO	CBF3C_YEAST	Centromere DNA-binding protein complex CBF3 subunit C (Kinetochore protein CTF13)	0.74	-	nuc	0	Nucleus	CBF3 complex [TAS] condensed nuclear chromosome kinetochore [TAS]			477
P12024 UniProt NPD GO	CHAO_DROME	Chaoptin precursor (Photoreceptor cell-specific membrane protein)	0.74	+	exc	1 *	Cell membrane; extracellular side. Extracellular surface of R-cell plasma membrane	plasma membrane [IDA]			1315

You are viewing entries 11701 to 11750 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.