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
Q9D2D7 UniProt NPD GO	ZN687_MOUSE	Zinc finger protein 687	0.81	-	nuc	0	Nucleus (Probable)				1237
Q8BKK5 UniProt NPD GO	ZN689_MOUSE	Zinc finger protein 689	0.81	-	nuc	0	Nucleus (Probable)				500
Q9Y2L8 UniProt NPD GO	ZFP95_HUMAN	Zinc finger protein 95 homolog (Zfp-95)	0.81	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			839
P60622 UniProt NPD GO	FOG1_BRARE	Zinc finger protein FOG1 (Friend of Gata1) (Zinc finger protein multitype 1) (Fragment)	0.81	+	nuc	0	Nucleus (By similarity)				224
Q5KEQ1 UniProt NPD GO	CET1_CRYNE	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.81	-	nuc	0	Nucleus (By similarity)				397
Q6CT22 UniProt NPD GO	CET1_KLULA	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.81	-	nuc	0	Nucleus (By similarity)				556
P78612 UniProt NPD GO	PALF_EMENI	pH-response regulator protein palF/RIM8	0.81	-	mit	0					775
O13967 UniProt NPD GO	BGS2_SCHPO	1,3-beta-glucan synthase component bgs2 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase) (M ...	0.80	-	end	16	Forespore; forespore inner membrane; multi-pass membrane protein	prospore membrane [IDA]			1894
Q9C0C2 UniProt NPD GO	TB182_HUMAN	182 kDa tankyrase 1-binding protein	0.80	-	nuc	0	Nucleus. Cytoplasm. Colocalizes with chromosomes during mitosis, and in the cytoplasm with cortical ...	cytoplasm [NAS] nuclear telomeric heterochromatin [NAS] nucleus [NAS]	607104		1729
P26986 UniProt NPD GO	2SSL_PICGL	2S seed storage-like protein precursor	0.80	-	nuc	0					172
Q9U761 UniProt NPD GO	RS6_AEDAE	40S ribosomal protein S6	0.80	+	nuc	0					346
P05754 UniProt NPD GO	RS8_YEAST	40S ribosomal protein S8 (S14) (YS9) (RP19)	0.80	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			199
Q63003 UniProt NPD GO	5E5_RAT	5E5 antigen	0.80	+	nuc	0	Nucleus				825
Q8ISQ3 UniProt NPD GO	RL24_BRABE	60S ribosomal protein L24	0.80	+	nuc	0					154
P52817 UniProt NPD GO	RL35_BABBO	60S ribosomal protein L35	0.80	-	nuc	0					123
P32611 UniProt NPD GO	RML2_YEAST	60S ribosomal protein RML2, mitochondrial precursor	0.80	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			393
Q9WVR1 UniProt NPD GO	INP5E_RAT	72 kDa inositol polyphosphate 5-phosphatase (EC 3.1.3.36) (Phosphatidylinositol-4,5-bisphosphate 5-p ...	0.80	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein; cytoplasmic side (B ...				647
Q02952 UniProt NPD GO	AKA12_HUMAN	A-kinase anchor protein 12 (A-kinase anchor protein 250 kDa) (AKAP 250) (Myasthenia gravis autoantig ...	0.80	-	nuc	0	Cytoplasm. May be part of the cortical cytoskeleton	cytoplasm [TAS]	604698		1781
O14672 UniProt NPD GO	ADA10_HUMAN	ADAM 10 precursor (EC 3.4.24.81) (A disintegrin and metalloproteinase domain 10) (Mammalian disinteg ...	0.80	-	exc	1	Cell membrane; single-pass type I membrane protein. Intracellular membrane; single-pass type I membr ...	cell surface [IDA] cytoplasm [ISS] Golgi apparatus [IDA] Golgi-associated vesicle [IDA] integral to plasma membrane [TAS] nucleus [ISS]	602192		748
Q10741 UniProt NPD GO	ADA10_BOVIN	ADAM 10 precursor (EC 3.4.24.81) (A disintegrin and metalloproteinase domain 10) (Mammalian disinteg ...	0.80	-	exc	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein. Cell membrane; single-pass typ ...	cell surface [ISS] cytoplasm [ISS] Golgi apparatus [ISS] Golgi-associated vesicle [ISS] nucleus [ISS]			748
O35674 UniProt NPD GO	ADA19_MOUSE	ADAM 19 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 19) (Meltrin beta)	0.80	-	end	1	Membrane; single-pass type I membrane protein				920
Q8TE60 UniProt NPD GO	ATS18_HUMAN	ADAMTS-18 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 18 ...	0.80	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		607512		1221
Q8WV99 UniProt NPD GO	ZFN2B_HUMAN	AN1-type zinc finger protein 2B	0.80	-	nuc	0				1X4V	257
Q9UTL8 UniProt NPD GO	AP3D_SCHPO	AP-3 complex subunit delta (Adapter-related protein complex 3 subunit delta) (Delta-adaptin 3) (AP-3 ...	0.80	+	nuc	1	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				834
O94761 UniProt NPD GO	RECQ4_HUMAN	ATP-dependent DNA helicase Q4 (EC 3.6.1.-) (RecQ protein-like 4) (RecQ4) (RTS)	0.80	-	nuc	0	Cytoplasm. Nucleus		603780		1208
Q6BPT8 UniProt NPD GO	DBP6_DEBHA	ATP-dependent RNA helicase DBP6 (EC 3.6.1.-)	0.80	-	nuc	0	Nucleus; nucleolus (By similarity)				679
Q59S50 UniProt NPD GO	DBP7_CANAL	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-)	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				727
Q5BBY1 UniProt NPD GO	HAS1_EMENI	ATP-dependent RNA helicase has1 (EC 3.6.1.-)	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				609
Q7SFC8 UniProt NPD GO	ROK1_NEUCR	ATP-dependent RNA helicase rok-1 (EC 3.6.1.-)	0.80	+	nuc	0	Nucleus; nucleolus (By similarity)				781
O46203 UniProt NPD GO	A32CD_DROME	Accessory gland protein Acp32CD precursor	0.80	-	nuc	0	Secreted protein (Probable)	extracellular region [TAS]			329
Q02067 UniProt NPD GO	ASCL1_MOUSE	Achaete-scute homolog 1 (Mash-1)	0.80	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			231
Q9BY76 UniProt NPD GO	ANGL4_HUMAN	Angiopoietin-related protein 4 precursor (Angiopoietin-like 4) (Hepatic fibrinogen/angiopoietin-rela ...	0.80	-	exc	0	Secreted protein	extracellular region [IEP]	605910		406
Q9P2S6 UniProt NPD GO	ANKY1_HUMAN	Ankyrin repeat and MYND domain-containing protein 1 (Testis-specific ankyrin-like protein 1) (Zinc-f ...	0.80	-	nuc	0					941
Q6NRD0 UniProt NPD GO	A13CA_XENLA	Ankyrin repeat domain-containing protein 13C-A	0.80	-	nuc	0					510
P33005 UniProt NPD GO	KALM_CHICK	Anosmin-1 precursor (Kallmann syndrome protein homolog)	0.80	+	mit	0	Cell surface (By similarity)				675
O70305 UniProt NPD GO	ATX2_MOUSE	Ataxin-2 (Spinocerebellar ataxia type 2 protein homolog)	0.80	-	nuc	0	Cytoplasm	perinuclear region [IDA]			1285
Q75D34 UniProt NPD GO	ATG21_ASHGO	Autophagy-related protein 21	0.80	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole; vacuolar ...				409
Q9D219 UniProt NPD GO	BCL9_MOUSE	B-cell lymphoma 9 protein (Bcl-9)	0.80	-	nuc	0	Nucleus				1425
P25917 UniProt NPD GO	CD19_CAVPO	B-lymphocyte antigen CD19 (Differentiation antigen CD19) (Fragment)	0.80	+	nuc	1	Membrane; single-pass type I membrane protein				430
Q9H4G0 UniProt NPD GO	E41L1_HUMAN	Band 4.1-like protein 1 (Neuronal protein 4.1) (4.1N)	0.80	-	nuc	0			602879		881
Q9Z2H5 UniProt NPD GO	E41L1_MOUSE	Band 4.1-like protein 1 (Neuronal protein 4.1) (4.1N)	0.80	-	nuc	0					879
O43491 UniProt NPD GO	E41L2_HUMAN	Band 4.1-like protein 2 (Generally expressed protein 4.1) (4.1G)	0.80	+	nuc	0		plasma membrane [TAS] spectrin [TAS]	603237		1005
P35612 UniProt NPD GO	ADDB_HUMAN	Beta-adducin (Erythrocyte adducin subunit beta)	0.80	+	nuc	0			102681		725
Q966W3 UniProt NPD GO	NDST_CAEEL	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.80	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				852
P11929 UniProt NPD GO	BSG2_DROME	Blastoderm-specific protein 25D	0.80	-	nuc	0					741
Q04906 UniProt NPD GO	BMP6_RAT	Bone morphogenetic protein 6 precursor (BMP-6) (VG-1-related protein) (VGR-1)	0.80	-	exc	0	Secreted protein (By similarity)				506
Q9H7B2 UniProt NPD GO	BXDC1_HUMAN	Brix domain-containing protein 1	0.80	-	nuc	0	Nucleus; nucleolus				306
Q8BTH8 UniProt NPD GO	KC1G1_MOUSE	Casein kinase I isoform gamma-1 (EC 2.7.11.1) (CKI-gamma 1)	0.80	+	nuc	0	Cytoplasm (By similarity)				459
Q99KF0 UniProt NPD GO	CAR14_MOUSE	Caspase recruitment domain-containing protein 14 (Bcl10-interacting MAGUK protein 2) (Bimp2)	0.80	-	nuc	0	Cytoplasm (By similarity)				999
O57538 UniProt NPD GO	P53_XIPHE	Cellular tumor antigen p53 (Tumor suppressor p53)	0.80	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				342

You are viewing entries 8751 to 8800 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.