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
Q9Y5K5 UniProt NPD GO	UCHL5_HUMAN	Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) (UCH-L5) (Ubiquitin thioesterase L5) ...	0.42	-	nuc	0					329
Q969Q1 UniProt NPD GO	TRI63_HUMAN	Ubiquitin ligase TRIM63 (EC 6.3.2.-) (Tripartite motif-containing protein 63) (Muscle-specific RING ...	0.42	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localizes to the M- and Z-lines in skeletal musc ...	cytoplasm [IDA] microtubule [NAS]	606131		353
Q8BH48 UniProt NPD GO	UBAP1_MOUSE	Ubiquitin-associated protein 1 (UBAP) (Ubiquitin-associated protein NAG20)	0.42	-	nuc	0					502
P53153 UniProt NPD GO	YGI5_YEAST	Uncharacterized endonuclease YGL085W (EC 3.1.-.-)	0.42	-	nuc	1 *		mitochondrion [IDA]			274
Q96MC5 UniProt NPD GO	CP045_HUMAN	Uncharacterized protein C16orf45	0.42	-	nuc	0					204
Q5E943 UniProt NPD GO	CA043_BOVIN	Uncharacterized protein C1orf43 homolog	0.42	-	nuc	1 *					253
Q80WB0 UniProt NPD GO	CT195_MOUSE	Uncharacterized protein C20orf195 homolog	0.42	-	cyt	0					326
Q09809 UniProt NPD GO	YAB9_SCHPO	Uncharacterized protein C2G11.09	0.42	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				796
P53336 UniProt NPD GO	YG5X_YEAST	Uncharacterized protein YGR283C	0.42	-	nuc	0		nucleolus [IDA]			341
P38790 UniProt NPD GO	YHM7_YEAST	Uncharacterized protein YHR067W	0.42	-	nuc	0					280
Q02205 UniProt NPD GO	YKY7_YEAST	Uncharacterized protein YKR007W	0.42	-	nuc	0		vacuolar membrane (sensu Fungi) [IDA]			184
Q06821 UniProt NPD GO	YP084_YEAST	Uncharacterized protein YPR084W	0.42	-	nuc	0					456
P54072 UniProt NPD GO	YL152_YEAST	Uncharacterized transporter YLR152C	0.42	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				576
P81401 UniProt NPD GO	VIP_BOVIN	VIP peptides precursor [Contains: Intestinal peptide PHI-27 (Peptide histidine isoleucinamide 27); V ...	0.42	-	exc	1 *	Secreted protein				170
P54611 UniProt NPD GO	VATE_DROME	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.42	-	cyt	0					226
O46563 UniProt NPD GO	VATH_BOVIN	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H) ...	0.42	-	cyt	0					483
Q9TVC1 UniProt NPD GO	VATH_PIG	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H) ...	0.42	-	cyt	0					483
O35485 UniProt NPD GO	VEGFB_RAT	Vascular endothelial growth factor B precursor (VEGF-B) (VEGF-related factor) (VRF)	0.42	-	exc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				207
Q3HXY4 UniProt NPD GO	NGFV_PSEPO	Venom nerve growth factor precursor (vNGF)	0.42	-	exc	0	Secreted protein				239
Q98993 UniProt NPD GO	VTXB_SYNVE	Verrucotoxin subunit beta (VTX subunit beta)	0.42	-	cyt	0	Secreted protein. However, no signal peptide has been found. This protein may follow a novel secreti ...				695
Q10271 UniProt NPD GO	YD37_SCHPO	Very hypothetical protein C13G7.07 in chromosome I	0.42	-	nuc	0					192
P98156 UniProt NPD GO	VLDLR_MOUSE	Very low-density lipoprotein receptor precursor (VLDL receptor) (VLDL-R)	0.42	-	exc	1	Membrane; single-pass type I membrane protein				873
Q91YD6 UniProt NPD GO	VILL_MOUSE	Villin-like protein (EF-6)	0.42	-	cyt	0					859
Q5J3M4 UniProt NPD GO	V1A13_RAT	Vomeronasal type-1 receptor A13	0.42	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				326
Q5F389 UniProt NPD GO	WWOX_CHICK	WW domain-containing oxidoreductase (EC 1.1.1.-)	0.42	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				414
P60029 UniProt NPD GO	IRPL1_PANTR	X-linked interleukin-1 receptor accessory protein-like 1 precursor (IL1RAPL-1) (Oligophrenin-4)	0.42	-	nuc	1	Membrane; single-pass type I membrane protein				696
Q7YQL9 UniProt NPD GO	IRPL1_PONPY	X-linked interleukin-1 receptor accessory protein-like 1 precursor (IL1RAPL-1) (Oligophrenin-4)	0.42	-	nuc	1	Membrane; single-pass type I membrane protein				696
Q9NZN1 UniProt NPD GO	IRPL1_HUMAN	X-linked interleukin-1 receptor accessory protein-like 1 precursor (IL1RAPL-1) (Oligophrenin-4) (Thr ...	0.42	-	nuc	1	Membrane; single-pass type I membrane protein		300206	1T3G	696
Q9R0X5 UniProt NPD GO	RPGR_MOUSE	X-linked retinitis pigmentosa GTPase regulator (mRpgr)	0.42	-	nuc	0	Golgi apparatus	cilium [IDA] cytoplasm [IDA] Golgi apparatus [IDA]			1001
Q6UX68 UniProt NPD GO	XKR5_HUMAN	XK-related protein 5	0.42	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				686
Q9H171 UniProt NPD GO	ZBP1_HUMAN	Z-DNA-binding protein 1 (Tumor stroma and activated macrophage protein DLM-1)	0.42	-	nuc	0			606750		429
Q8SV95 UniProt NPD GO	Z6B5_ENCCU	Zinc finger C2H2 protein ECU06_1150	0.42	-	nuc	0					145
Q6NPN3 UniProt NPD GO	ZFNL3_ARATH	Zinc finger CCCH domain-containing protein ZFN-like 3	0.42	-	nuc	0	Nucleus (By similarity)				465
Q91X45 UniProt NPD GO	ZBTB3_MOUSE	Zinc finger and BTB domain-containing protein 3	0.42	-	nuc	0	Nucleus (Potential)				518
Q96C00 UniProt NPD GO	ZBTB9_HUMAN	Zinc finger and BTB domain-containing protein 9	0.42	-	nuc	0	Nucleus (Potential)				473
Q8CDC7 UniProt NPD GO	ZBTB9_MOUSE	Zinc finger and BTB domain-containing protein 9	0.42	-	nuc	0	Nucleus (Potential)				459
P17023 UniProt NPD GO	ZNF19_HUMAN	Zinc finger protein 19 (Zinc finger protein KOX12)	0.42	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194525		458
P17027 UniProt NPD GO	ZNF23_HUMAN	Zinc finger protein 23 (Zinc finger protein 359) (Zinc finger protein KOX16)	0.42	-	nuc	0	Nucleus (Potential)		194527		643
Q3ZCT1 UniProt NPD GO	ZF260_HUMAN	Zinc finger protein 260 homolog (Zfp-260)	0.42	-	nuc	0	Nucleus				409
Q3SYV7 UniProt NPD GO	ZN345_BOVIN	Zinc finger protein 345	0.42	-	nuc	0	Nucleus (Probable)				487
Q86VK4 UniProt NPD GO	ZN410_HUMAN	Zinc finger protein 410 (Zinc finger protein APA-1) (Another partner for ARF 1)	0.42	-	nuc	0	Nucleus (Probable)				478
Q8TB69 UniProt NPD GO	ZN519_HUMAN	Zinc finger protein 519	0.42	-	nuc	0	Nucleus (Probable)				540
Q8IVC4 UniProt NPD GO	ZN584_HUMAN	Zinc finger protein 584	0.42	-	nuc	0	Nucleus (Probable)				421
Q5SXM1 UniProt NPD GO	ZN678_HUMAN	Zinc finger protein 678	0.42	-	nuc	0	Nucleus (Probable)				525
P10075 UniProt NPD GO	GLI4_HUMAN	Zinc finger protein GLI4 (Krueppel-related zinc finger protein 4) (Protein HKR4)	0.42	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	165280		376
P53303 UniProt NPD GO	ZPR1_YEAST	Zinc-finger protein ZPR1	0.42	-	nuc	0	Cytoplasm. Nucleus. Translocates to the nucleus after nutrient stimulation	cytoplasm [IDA] nucleus [IDA]			486
O16999 UniProt NPD GO	ZPR1_CAEEL	Zinc-finger protein ZPR1 homolog	0.42	-	nuc	0	Nucleus (Potential)				455
P19198 UniProt NPD GO	CAP1_DICDI	cAMP-binding protein CABP1A/CABP1B (CABP1 protein)	0.42	-	nuc	0					333
Q5BGN2 UniProt NPD GO	YTH1_EMENI	mRNA 3'-end-processing protein yth1	0.42	-	nuc	0	Nucleus (By similarity)				254
Q9DCE5 UniProt NPD GO	PK1IP_MOUSE	p21-activated protein kinase-interacting protein 1 (PAK1-interacting protein 1) (Putative PAK inhibi ...	0.42	+	mit	0	Nucleus; nucleolus (By similarity)				382

You are viewing entries 30801 to 30850 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.