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
Q96RI1 UniProt NPD GO	NR1H4_HUMAN	Bile acid receptor (Farnesoid X-activated receptor) (Farnesol receptor HRR-1) (Retinoid X receptor-i ...	0.67	-	nuc	0	Nucleus (Probable)		603826	1OSK	486
Q6GLC7 UniProt NPD GO	BOREA_XENTR	Borealin (Cell division cycle-associated protein 8)	0.67	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				279
Q29543 UniProt NPD GO	RNBR_SHEEP	Brain ribonuclease (EC 3.1.27.-) (BRB)	0.67	-	nuc	0	Secreted protein				143
Q68EF6 UniProt NPD GO	BEGIN_MOUSE	Brain-enriched guanylate kinase-associated protein	0.67	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				600
Q6R6L0 UniProt NPD GO	BEGIN_SHEEP	Brain-enriched guanylate kinase-associated protein	0.67	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				653
Q9Y6D5 UniProt NPD GO	BIG2_HUMAN	Brefeldin A-inhibited guanine nucleotide-exchange protein 2 (Brefeldin A-inhibited GEP 2)	0.67	-	cyt	0		cytosol [IDA] Golgi membrane [IDA] membrane [IDA]	605371		1785
P53755 UniProt NPD GO	BSC5_YEAST	Bypass of stop codon protein 5	0.67	-	nuc	0					489
P16236 UniProt NPD GO	REL_CHICK	C-Rel proto-oncogene protein (C-Rel protein) (p68)	0.67	+	nuc	0	Nucleus	cytoplasm [TAS]		1GJI	598
P15037 UniProt NPD GO	ETS2_MOUSE	C-ets-2 protein	0.67	+	nuc	0	Nucleus				468
P25578 UniProt NPD GO	PGS1_YEAST	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5) (Phosphatidylglycero ...	0.67	-	mit	0	Mitochondrion	mitochondrion [IDA]			521
Q95PZ0 UniProt NPD GO	CSN6_CAEEL	COP9 signalosome complex subunit 6 (Signalosome subunit 6)	0.67	+	nuc	0	Cytoplasm. Nucleus				426
Q9R0M0 UniProt NPD GO	CELR2_MOUSE	Cadherin EGF LAG seven-pass G-type receptor 2 precursor (Flamingo 1) (mFmi1)	0.67	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [ISS]			2920
Q43531 UniProt NPD GO	CCAMK_LILLO	Calcium and calcium/calmodulin-dependent serine/threonine-protein kinase (EC 2.7.11.17) (LlCCaMK)	0.67	+	nuc	0					520
P49069 UniProt NPD GO	CAMLG_HUMAN	Calcium signal-modulating cyclophilin ligand (CAML)	0.67	-	nuc	0	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]	601118		296
Q92179 UniProt NPD GO	CHST3_CHICK	Carbohydrate sulfotransferase 3 (EC 2.8.2.17) (Chondroitin 6-O-sulfotransferase 1) (C6ST-1) (C6ST)	0.67	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				458
Q62762 UniProt NPD GO	KC1G2_RAT	Casein kinase I isoform gamma-2 (EC 2.7.11.1) (CKI-gamma 2)	0.67	-	nuc	0	Cytoplasm				415
O89110 UniProt NPD GO	CASP8_MOUSE	Caspase-8 precursor (EC 3.4.22.-) (CASP-8) [Contains: Caspase-8 subunit p18; Caspase-8 subunit p10]	0.67	-	nuc	0		cytoplasm [IDA] Noc1p-Noc2p complex [IMP] nucleus [IDA]			480
Q12748 UniProt NPD GO	CTF3_YEAST	Central kinetochore subunit CTF3 (Chromosome transmission fidelity protein 3) (Chromosome loss prote ...	0.67	-	nuc	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA]			733
P0C0A3 UniProt NPD GO	CHMP6_MOUSE	Charged multivesicular body protein 6 (Chromatin-modifying protein 6)	0.67	-	nuc	0	Intracytoplasmic membrane (By similarity). Endosome; endosomal membrane; lipid-anchor (By similarity ...				199
P32976 UniProt NPD GO	RR14_CHLVU	Chloroplast 30S ribosomal protein S14	0.67	-	nuc	0	Plastid; chloroplast				100
P41648 UniProt NPD GO	RR15_PINTH	Chloroplast 30S ribosomal protein S15	0.67	-	nuc	0	Plastid; chloroplast				88
Q9BBR1 UniProt NPD GO	RR18_LOTJA	Chloroplast 30S ribosomal protein S18	0.67	-	nuc	0	Plastid; chloroplast				104
P49170 UniProt NPD GO	RR18_SECCE	Chloroplast 30S ribosomal protein S18	0.67	-	nuc	0	Plastid; chloroplast				170
Q95H55 UniProt NPD GO	RR18_WHEAT	Chloroplast 30S ribosomal protein S18	0.67	-	nuc	0	Plastid; chloroplast				170
P36467 UniProt NPD GO	RR4_PENVI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.67	-	mit	0	Plastid; chloroplast				196
Q5SCY6 UniProt NPD GO	RR7_HUPLU	Chloroplast 30S ribosomal protein S7	0.67	-	nuc	0	Plastid; chloroplast				150
P26566 UniProt NPD GO	RK20_MAIZE	Chloroplast 50S ribosomal protein L20	0.67	-	mit	0	Plastid; chloroplast				118
Q9MUP7 UniProt NPD GO	RK20_MESVI	Chloroplast 50S ribosomal protein L20	0.67	-	nuc	0	Plastid; chloroplast				115
Q6ENA9 UniProt NPD GO	RK32_ORYNI	Chloroplast 50S ribosomal protein L32	0.67	-	mit	0	Plastid; chloroplast				59
O95931 UniProt NPD GO	CBX7_HUMAN	Chromobox protein homolog 7	0.67	-	nuc	0	Nucleus		608457		251
Q29482 UniProt NPD GO	CLUS_HORSE	Clusterin precursor [Contains: Clusterin beta chain; Clusterin alpha chain]	0.67	-	exc	0	Secreted protein (By similarity)				449
Q8HZ59 UniProt NPD GO	CCHCR_GORGO	Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein)	0.67	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				782
Q9D4H8 UniProt NPD GO	CUL2_MOUSE	Cullin-2 (CUL-2)	0.67	-	cyt	0					745
P51947 UniProt NPD GO	CCNH_XENLA	Cyclin-H (MO15-associated protein) (p36)	0.67	+	mit	0	Nucleus				323
P46529 UniProt NPD GO	CDN1B_MUSVI	Cyclin-dependent kinase inhibitor 1B (Cyclin-dependent kinase inhibitor p27) (p27Kip1) (Fragment)	0.67	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear and cytoplasmic in quiescent cells. Upon ...				178
Q00554 UniProt NPD GO	CFTR_RABIT	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.67	-	end	11	Membrane; multi-pass membrane protein				1480
Q5D1Z7 UniProt NPD GO	CFTR_TRIVU	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.67	-	end	11	Membrane; multi-pass membrane protein				1478
Q02928 UniProt NPD GO	CP4AB_HUMAN	Cytochrome P450 4A11 precursor (EC 1.14.15.3) (CYPIVA11) (Fatty acid omega-hydroxylase) (P-450 HK om ...	0.67	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]	601310		519
P63035 UniProt NPD GO	CYH2_RAT	Cytohesin-2 (CLM2) (ARF nucleotide-binding site opener) (ARNO protein) (SEC7 homolog B)	0.67	-	cyt	0					400
P63034 UniProt NPD GO	CYH2_MOUSE	Cytohesin-2 (CLM2) (SEC7 homolog B) (msec7-2)	0.67	-	cyt	0				1U29	400
O43739 UniProt NPD GO	CYH3_HUMAN	Cytohesin-3 (ARF nucleotide-binding site opener 3) (ARNO3 protein) (General receptor of phosphoinosi ...	0.67	+	cyt	0		membrane fraction [TAS] plasma membrane [TAS]	605081		400
Q6E3D0 UniProt NPD GO	CPB1_CAEBR	Cytoplasmic polyadenylation element-binding protein 1	0.67	-	nuc	0					585
Q8BR07 UniProt NPD GO	BICD1_MOUSE	Cytoskeleton-like bicaudal D protein homolog 1	0.67	-	nuc	0	Golgi apparatus				835
P53168 UniProt NPD GO	DUO1_YEAST	DASH complex subunit DUO1 (Outer kinetochore protein DUO1) (Death upon overproduction protein 1)	0.67	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle microtubule [IDA] spindle pole body [IDA]			247
Q8GUG7 UniProt NPD GO	RH50_ARATH	DEAD-box ATP-dependent RNA helicase 50 (EC 3.6.1.-)	0.67	-	mit	0					781
Q8K382 UniProt NPD GO	DEN1A_MOUSE	DENN domain-containing protein 1A	0.67	-	nuc	0					1016
Q12086 UniProt NPD GO	DIN7_YEAST	DNA damage-inducible protein DIN7	0.67	+	cyt	0	Nucleus (Potential)	mitochondrion [IDA]			430
P42118 UniProt NPD GO	TDT_XENLA	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.67	+	cyt	0	Nucleus (By similarity)				507
Q5R4W3 UniProt NPD GO	DPOE3_PONPY	DNA polymerase epsilon subunit 3 (EC 2.7.7.7) (DNA polymerase II subunit 3) (DNA polymerase epsilon ...	0.67	-	nuc	0	Nucleus (Potential)				147
Q9NRF9 UniProt NPD GO	DPOE3_HUMAN	DNA polymerase epsilon subunit 3 (EC 2.7.7.7) (DNA polymerase II subunit 3) (DNA polymerase epsilon ...	0.67	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	607267		147

You are viewing entries 15151 to 15200 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.