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
Q757A7 UniProt NPD GO	ATG17_ASHGO	Autophagy-related protein 17	0.58	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				413
Q5IF00 UniProt NPD GO	ATG28_PICPA	Autophagy-related protein 28	0.58	-	nuc	0					612
Q9FGV1 UniProt NPD GO	ARFH_ARATH	Auxin response factor 8	0.58	-	nuc	0	Nucleus				811
Q60739 UniProt NPD GO	BAG1_MOUSE	BAG family molecular chaperone regulator 1 (BCL-2-binding athanogene-1) (BAG-1)	0.58	+	nuc	0		cytosol [IDA] nucleus [IDA]		1I6Z	355
Q62210 UniProt NPD GO	BIRC2_MOUSE	Baculoviral IAP repeat-containing protein 2 (Inhibitor of apoptosis protein 2) (MIAP2) (MIAP-2)	0.58	-	nuc	0	Cytoplasm (Potential)				612
Q03376 UniProt NPD GO	BAR3_CHITE	Balbiani ring protein 3 precursor	0.58	-	exc	0	Secreted protein				1700
P59101 UniProt NPD GO	SCX_CHICK	Basic helix-loop-helix transcription factor scleraxis	0.58	-	nuc	0	Nucleus (By similarity)				187
Q14457 UniProt NPD GO	BCN1_HUMAN	Beclin-1 (Coiled-coil myosin-like BCL2-interacting protein) (Protein GT197)	0.58	-	mit	0	Cytoplasm (Potential). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity). ...		604378		450
O54905 UniProt NPD GO	B3GT2_MOUSE	Beta-1,3-galactosyltransferase 2 (EC 2.4.1.-) (Beta-1,3-GalTase 2) (Beta3Gal-T2) (UDP-Gal:betaGlcNAc ...	0.58	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				422
Q8R087 UniProt NPD GO	B4GT7_MOUSE	Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-) (Beta-1,4-GalTase 7) (Beta4Gal-T7) (b4Gal-T7) (UDP-gal ...	0.58	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				327
Q60V90 UniProt NPD GO	NDST_CAEBR	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.58	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				855
P23118 UniProt NPD GO	BIND_STRFN	Bindin precursor	0.58	-	exc	0	Acrosome; acrosomal lumen				485
Q5PPZ5 UniProt NPD GO	BIN3_XENLA	Bridging integrator 3 homolog	0.58	-	nuc	0					252
Q9ERE9 UniProt NPD GO	JIP2_MOUSE	C-jun-amino-terminal kinase-interacting protein 2 (JNK-interacting protein 2) (JIP-2) (JNK MAP kinas ...	0.58	-	nuc	0	Cytoplasm. Accumulates in cell surface projections (By similarity)	cell soma [IDA] cytoplasm [ISS]			830
Q76KW6 UniProt NPD GO	ANFC_ACITR	C-type natriuretic peptide precursor	0.58	-	exc	0	Secreted protein				150
Q29423 UniProt NPD GO	CD44_BOVIN	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.58	-	end	1	Membrane; single-pass type I membrane protein				366
P70412 UniProt NPD GO	CUZD1_MOUSE	CUB and zona pellucida-like domain-containing protein 1 precursor (Integral membrane-associated prot ...	0.58	-	nuc	1	Membrane; single-pass type I membrane protein (Potential). Associated with zymogen granule membranes ...	integral to membrane [NAS] zymogen granule membrane [IDA]			606
Q92879 UniProt NPD GO	CUGB1_HUMAN	CUG triplet repeat RNA-binding protein 1 (CUG-BP1) (RNA-binding protein BRUNOL-2) (Deadenylation fac ...	0.58	-	nuc	0	Nucleus	nucleus [NAS] ribonucleoprotein complex [NAS]	601074	2CPZ	486
P28659 UniProt NPD GO	CUGB1_MOUSE	CUG triplet repeat RNA-binding protein 1 (CUG-BP1) (RNA-binding protein BRUNOL-2) (Deadenylation fac ...	0.58	-	nuc	0	Nucleus (By similarity)	cytoplasm [TAS] nucleus [ISS] ribonucleoprotein complex [ISS] soluble fraction [IDA]			486
O88278 UniProt NPD GO	CELR3_RAT	Cadherin EGF LAG seven-pass G-type receptor 3 precursor (Multiple epidermal growth factor-like domai ...	0.58	-	end	6 *	Membrane; multi-pass membrane protein				3313
O13833 UniProt NPD GO	CID1_SCHPO	Caffeine-induced death protein 1	0.58	-	nuc	1		cytoplasm [IDA]			405
Q99MP3 UniProt NPD GO	CALCB_MOUSE	Calcitonin gene-related peptide 2 precursor (Calcitonin gene-related peptide II) (CGRP-II) (Beta-typ ...	0.58	-	vac	1 *	Secreted protein				130
P10093 UniProt NPD GO	CALCB_RAT	Calcitonin gene-related peptide 2 precursor (Calcitonin gene-related peptide II) (CGRP-II) (Beta-typ ...	0.58	-	exc	0	Secreted protein				134
Q08460 UniProt NPD GO	KCMA1_MOUSE	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.58	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1209
Q90ZC7 UniProt NPD GO	KCMA1_XENLA	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.58	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1196
Q8NET6 UniProt NPD GO	CHSTD_HUMAN	Carbohydrate sulfotransferase 13 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 3) (Chondroitin 4-su ...	0.58	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [NAS]			341
Q9QZL2 UniProt NPD GO	CHST3_RAT	Carbohydrate sulfotransferase 3 (EC 2.8.2.17) (Chondroitin 6-O-sulfotransferase 1) (C6ST-1) (Galacto ...	0.58	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				474
P42573 UniProt NPD GO	CED3_CAEEL	Cell death protein 3 precursor (EC 3.4.22.-) [Contains: Cell death protein 3 subunit 1; Cell death p ...	0.58	+	nuc	0					503
Q12834 UniProt NPD GO	CDC20_HUMAN	Cell division cycle protein 20 homolog (p55CDC)	0.58	-	nuc	0		spindle [TAS]	603618		499
Q3T0L1 UniProt NPD GO	CENPH_BOVIN	Centromere protein H (Kinetochore protein CENP-H)	0.58	-	nuc	0	Nucleus. Associates with active centromere-kinetochore complexes throughout the cell cycle. Colocali ...				244
O13473 UniProt NPD GO	CBF5_KLULA	Centromere/microtubule-binding protein CBF5 (Centromere-binding factor 5) (Small nucleolar RNP prote ...	0.58	+	nuc	0	Nucleus; nucleolus (By similarity)				474
Q6XL73 UniProt NPD GO	DNJ39_ARATH	Chaperone protein dnaJ 39 (Protein ARG1-LIKE2) (AtARL2) (AtJ39) (AtDjC39)	0.58	-	mit	0	Membrane; peripheral membrane protein (Potential)				414
Q8WHZ0 UniProt NPD GO	RR11_PSINU	Chloroplast 30S ribosomal protein S11	0.58	+	nuc	0	Plastid; chloroplast				130
Q85CU9 UniProt NPD GO	RR14_ANTFO	Chloroplast 30S ribosomal protein S14	0.58	-	nuc	0	Plastid; chloroplast				100
P32975 UniProt NPD GO	RR4_CHLVU	Chloroplast 30S ribosomal protein S4	0.58	-	nuc	0	Plastid; chloroplast				207
O20230 UniProt NPD GO	RR4_HYMLI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.58	-	nuc	0	Plastid; chloroplast				182
Q7YJT7 UniProt NPD GO	RK2_CALFE	Chloroplast 50S ribosomal protein L2	0.58	+	nuc	0	Plastid; chloroplast				273
P17788 UniProt NPD GO	RK2_MAIZE	Chloroplast 50S ribosomal protein L2	0.58	+	nuc	0	Plastid; chloroplast				273
Q6EVY5 UniProt NPD GO	RK2_NYMAL	Chloroplast 50S ribosomal protein L2	0.58	+	nuc	0	Plastid; chloroplast				273
Q85WS5 UniProt NPD GO	RK2_PINKO	Chloroplast 50S ribosomal protein L2	0.58	-	nuc	0	Plastid; chloroplast				276
Q6L3B9 UniProt NPD GO	RK2_SACHY	Chloroplast 50S ribosomal protein L2	0.58	+	nuc	0	Plastid; chloroplast				273
Q6ENS1 UniProt NPD GO	RK2_SACOF	Chloroplast 50S ribosomal protein L2	0.58	+	nuc	0	Plastid; chloroplast				273
Q85FI9 UniProt NPD GO	RK36_ADICA	Chloroplast 50S ribosomal protein L36	0.58	-	nuc	0	Plastid; chloroplast				37
Q07979 UniProt NPD GO	RSC58_YEAST	Chromatin structure remodeling complex protein RSC58 (Remodel the structure of chromatin complex sub ...	0.58	+	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			502
P45968 UniProt NPD GO	YNZ8_CAEEL	Chromo domain-containing protein T09A5.8	0.58	-	nuc	0	Nucleus (Potential)				339
Q6NWC6 UniProt NPD GO	CPSF6_BRARE	Cleavage and polyadenylation specificity factor 6	0.58	+	nuc	0	Nucleus (By similarity)				545
Q91VN4 UniProt NPD GO	CHCH6_MOUSE	Coiled-coil-helix-coiled-coil-helix domain-containing protein 6	0.58	-	nuc	0					273
Q00685 UniProt NPD GO	CO3_LAMJA	Complement C3 precursor [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphyla ...	0.58	+	cyt	0					1673
O42637 UniProt NPD GO	CIA84_NEUCR	Complex I intermediate-associated protein 84, mitochondrial precursor	0.58	-	mit	0	Mitochondrion				797
Q13951 UniProt NPD GO	PEBB_HUMAN	Core-binding factor subunit beta (CBF-beta) (Polyomavirus enhancer-binding protein 2 beta subunit) ( ...	0.58	-	nuc	0	Nucleus (Potential)		121360	1H9D	182

You are viewing entries 20051 to 20100 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.