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
P34692 UniProt NPD GO	U183_CAEEL	UPF0183 protein T01G9.2	0.30	-	cyt	0					422
P38829 UniProt NPD GO	YHS2_YEAST	UPF0195 protein YHR122W	0.30	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			231
Q9CR37 UniProt NPD GO	CT149_MOUSE	UPF0362 protein C20orf149 homolog	0.30	-	nuc	0					115
Q8SPH5 UniProt NPD GO	UCRH_MACFA	Ubiquinol-cytochrome c reductase complex 11 kDa protein, mitochondrial precursor (EC 1.10.2.2) (Mito ...	0.30	-	nuc	0	Mitochondrion; mitochondrial inner membrane				91
Q9D855 UniProt NPD GO	UCR6_MOUSE	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VI)	0.30	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			110
O14949 UniProt NPD GO	UCRQ_HUMAN	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.30	-	cyt	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex III (sensu Eukary... [NAS]			81
P51135 UniProt NPD GO	UCRI5_TOBAC	Ubiquinol-cytochrome c reductase iron-sulfur subunit 5, mitochondrial precursor (EC 1.10.2.2) (Riesk ...	0.30	-	mit	1	Mitochondrion; mitochondrial inner membrane				268
Q5RBK6 UniProt NPD GO	COQ5_PONPY	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.30	-	mit	0	Mitochondrion (By similarity)				327
Q6PGH0 UniProt NPD GO	UBTD2_MOUSE	Ubiquitin domain-containing protein 2	0.30	-	nuc	0	Cytoplasm (By similarity)				234
P20973 UniProt NPD GO	UBE11_WHEAT	Ubiquitin-activating enzyme E1 1	0.30	-	cyt	0					1051
P31251 UniProt NPD GO	UBE12_WHEAT	Ubiquitin-activating enzyme E1 2	0.30	-	cyt	0					1051
Q3MHP1 UniProt NPD GO	UB2L3_BOVIN	Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) (Ubiquitin-protein ligase L3) (Ubiquitin carrier pr ...	0.30	-	nuc	0					154
P68036 UniProt NPD GO	UB2L3_HUMAN	Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) (Ubiquitin-protein ligase L3) (Ubiquitin carrier pr ...	0.30	-	nuc	0		ubiquitin ligase complex [TAS]	603721	1FBV	154
P68037 UniProt NPD GO	UB2L3_MOUSE	Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) (Ubiquitin-protein ligase L3) (Ubiquitin carrier pr ...	0.30	-	nuc	0		ubiquitin ligase complex [ISS]			154
P09003 UniProt NPD GO	MI25_TOBAC	Uncharacterized mitochondrial 22 kDa protein (ORF 25)	0.30	-	end	1 *					198
Q9NVR5 UniProt NPD GO	CN104_HUMAN	Uncharacterized protein C14orf104	0.30	-	nuc	0					328
Q8VCC6 UniProt NPD GO	CT160_MOUSE	Uncharacterized protein C20orf160 homolog	0.30	-	cyt	0					192
Q96LM9 UniProt NPD GO	CT173_HUMAN	Uncharacterized protein C20orf173	0.30	-	nuc	0					149
Q9D4G1 UniProt NPD GO	CU062_MOUSE	Uncharacterized protein C21orf62 homolog	0.30	-	nuc	1 *					230
Q9BV87 UniProt NPD GO	CB024_HUMAN	Uncharacterized protein C2orf24	0.30	-	cyt	0					410
Q78IK4 UniProt NPD GO	CX033_MOUSE	Uncharacterized protein CXorf33 homolog precursor	0.30	-	nuc	0	Secreted protein (Potential)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			265
P34558 UniProt NPD GO	YNP5_CAEEL	Uncharacterized protein T05G5.5	0.30	-	mit	1					237
P40003 UniProt NPD GO	YEA5_YEAST	Uncharacterized protein YEL005C	0.30	-	nuc	0		cytoplasm [IDA]			282
Q3E7Z3 UniProt NPD GO	YI018_YEAST	Uncharacterized protein YIR018C-A	0.30	-	nuc	0					45
Q3E7A9 UniProt NPD GO	YM194_YEAST	Uncharacterized protein YMR194C-B	0.30	-	nuc	0					73
P53873 UniProt NPD GO	YNS7_YEAST	Uncharacterized protein YNL187W	0.30	-	cyt	0	Nucleus	nucleus [IMP]			357
Q3E835 UniProt NPD GO	YO086_YEAST	Uncharacterized protein YOL086W-A	0.30	-	cyt	0					90
Q08270 UniProt NPD GO	YO131_YEAST	Uncharacterized protein YOL131W	0.30	-	nuc	0					108
Q9S720 UniProt NPD GO	THL1_ARATH	Unknown thylakoid lumen protein, chloroplast precursor	0.30	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				247
P97931 UniProt NPD GO	UNG_MOUSE	Uracil-DNA glycosylase (UDG)	0.30	-	mit	0	Isoform 1: Mitochondrion. Isoform 2: Nucleus	mitochondrion [IDA] nucleus [IDA]			306
Q9HA47 UniProt NPD GO	UCK1_HUMAN	Uridine-cytidine kinase 1 (EC 2.7.1.48) (UCK 1) (Uridine monophosphokinase 1) (Cytidine monophosphok ...	0.30	-	cyt	0			609328		277
P55895 UniProt NPD GO	RAG2_HUMAN	V(D)J recombination-activating protein 2 (RAG-2)	0.30	-	cyt	0	Nucleus	nucleus [NAS]	603554		527
Q9D1C8 UniProt NPD GO	VPS28_MOUSE	VPS28 protein homolog (Caspase-activated DNase inhibitor that interacts with ASK1) (CIIA)	0.30	-	cyt	0					221
Q43433 UniProt NPD GO	VATB2_GOSHI	Vacuolar ATP synthase subunit B isoform 2 (EC 3.6.3.14) (V-ATPase B subunit 2) (Vacuolar proton pump ...	0.30	-	cyt	0					386
Q5RCS8 UniProt NPD GO	VATD_PONPY	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.30	-	cyt	0					247
Q9Y5K8 UniProt NPD GO	VATD_HUMAN	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit) ...	0.30	-	cyt	0					247
O97755 UniProt NPD GO	VATD_RABIT	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit) ...	0.30	-	cyt	0					247
P22203 UniProt NPD GO	VATE_YEAST	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.30	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein	hydrogen-transporting ATPase V1 domain [TAS] vacuolar membrane (sensu Fungi) [TAS]			232
P78713 UniProt NPD GO	VATG_NEUCR	Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G subunit) ...	0.30	-	nuc	0					115
O13753 UniProt NPD GO	VA0D_SCHPO	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.30	-	cyt	0					343
Q4G0F5 UniProt NPD GO	VP26B_HUMAN	Vacuolar protein sorting 26B (Vesicle protein sorting 26B)	0.30	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)		610027		336
Q6AX45 UniProt NPD GO	VPS25_XENLA	Vacuolar protein sorting protein 25	0.30	-	cyt	0	Cytoplasm (By similarity)				174
P20949 UniProt NPD GO	VSY3_TRYCO	Variant surface glycoprotein YnAT 1.3 precursor (VSG)	0.30	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				413
Q6EMK4 UniProt NPD GO	VASN_HUMAN	Vasorin precursor (Protein Slit-like 2)	0.30	-	end	1	Membrane; single-pass type I membrane protein (Probable). Secreted protein		608843		673
Q8MMH3 UniProt NPD GO	VPR2_PIMHY	Venom protein 2 precursor	0.30	-	mit	0	Secreted protein				488
Q9Y7Q0 UniProt NPD GO	YQ66_SCHPO	Very hypothetical protein C191.06 in chromosome III	0.30	-	nuc	0					138
P40163 UniProt NPD GO	YNU3_YEAST	Very hypothetical protein YNL203C	0.30	-	nuc	0					203
Q8MR62 UniProt NPD GO	VIAF1_DROME	Viral IAP-associated factor homolog	0.30	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			240
Q64259 UniProt NPD GO	VHL_RAT	Von Hippel-Lindau disease tumor suppressor (pVHL)	0.30	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Nucleus (By simila ...	cytosol [IDA] nucleus [IDA] transcription factor complex [TAS]			185
Q9JJA4 UniProt NPD GO	WDR12_MOUSE	WD repeat protein 12 (YTM1 homolog)	0.30	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleus [IDA]			423

You are viewing entries 40851 to 40900 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.