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
O19131 UniProt NPD GO	TNR1A_BOVIN	Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (TNFR-I) (p55 ...	0.48	-	exc	1	Membrane; single-pass type I membrane protein				471
Q8BX35 UniProt NPD GO	TNR27_MOUSE	Tumor necrosis factor receptor superfamily member 27 (X-linked ectodysplasin-A2 receptor) (EDA-A2 re ...	0.48	-	nuc	1	Membrane; single-pass type III membrane protein (By similarity)	integral to membrane [ISS]			297
Q60846 UniProt NPD GO	TNR8_MOUSE	Tumor necrosis factor receptor superfamily member 8 precursor (CD30L receptor) (Lymphocyte activatio ...	0.48	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				498
O17446 UniProt NPD GO	TY3H_SCHMA	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.48	-	nuc	0					465
Q07014 UniProt NPD GO	LYN_RAT	Tyrosine-protein kinase Lyn (EC 2.7.10.2)	0.48	-	nuc	0		cytoplasm [ISS] nucleus [ISS]			511
Q9Z138 UniProt NPD GO	ROR2_MOUSE	Tyrosine-protein kinase transmembrane receptor ROR2 precursor (EC 2.7.10.1) (Neurotrophic tyrosine k ...	0.48	-	nuc	1	Membrane; single-pass type I membrane protein				944
P27574 UniProt NPD GO	PYP1_SCHPO	Tyrosine-protein phosphatase 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1) (PTPase 1)	0.48	-	nuc	0	Cytoplasm				550
Q5NVD0 UniProt NPD GO	PRP4_PONPY	U4/U6 small nuclear ribonucleoprotein Prp4 (U4/U6 snRNP 60 kDa protein) (WD splicing factor Prp4)	0.48	-	mit	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...				521
Q9JJP9 UniProt NPD GO	UBQL1_RAT	Ubiquilin-1 (Protein linking IAP with cytoskeleton 1) (PLIC-1)	0.48	-	nuc	0	Nucleus (By similarity). Cytoplasm. Detected in neuronal processes and at synapses			1KJV	582
Q99NB8 UniProt NPD GO	UBQL4_MOUSE	Ubiquilin-4 (Ataxin-1 ubiquitin-like-interacting protein A1U)	0.48	-	nuc	0	Nucleus (By similarity). Cytoplasm. May associate with the endoplasmic reticulum	cytoplasm [ISS] cytosol [IDA] endoplasmic reticulum membrane [IDA] nucleus [ISS]			596
Q6FQK7 UniProt NPD GO	UBC6_CANGA	Ubiquitin-conjugating enzyme E2 6 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC6) (Ubiquitin carrier p ...	0.48	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane (By similarity)				246
P49459 UniProt NPD GO	UBE2A_HUMAN	Ubiquitin-conjugating enzyme E2 A (EC 6.3.2.19) (Ubiquitin-protein ligase A) (Ubiquitin carrier prot ...	0.48	-	nuc	0			312180		152
Q9Z255 UniProt NPD GO	UBE2A_MOUSE	Ubiquitin-conjugating enzyme E2 A (EC 6.3.2.19) (Ubiquitin-protein ligase A) (Ubiquitin carrier prot ...	0.48	-	nuc	0		chromatin [IDA]			152
P14682 UniProt NPD GO	UBC3_YEAST	Ubiquitin-conjugating enzyme E2-34 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.48	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nuclear ubiquitin ligase complex [TAS] nucleus [IDA] SCF ubiquitin ligase complex [IMP]			295
Q96S82 UniProt NPD GO	UBL7_HUMAN	Ubiquitin-like protein 7 (Ubiquitin-like protein SB132) (Bone marrow stromal cell ubiquitin-like pro ...	0.48	-	nuc	0			609748	2CWB	380
Q9VZI3 UniProt NPD GO	UN112_DROME	Unc-112-related protein (Fermitin-1)	0.48	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS]			708
Q9BQN1 UniProt NPD GO	CT128_HUMAN	Uncharacterized protein C20orf128	0.48	-	nuc	0					733
Q9BVV2 UniProt NPD GO	CT195_HUMAN	Uncharacterized protein C20orf195	0.48	-	cyt	0					318
Q9CXC3 UniProt NPD GO	CT072_MOUSE	Uncharacterized protein C20orf72 homolog	0.48	-	mit	0					338
P48569 UniProt NPD GO	YD183_YEAST	Uncharacterized protein YDL183C	0.48	-	mit	0					320
P53255 UniProt NPD GO	YG2M_YEAST	Uncharacterized protein YGR093W	0.48	-	nuc	0		nucleus [IDA]			507
Q06058 UniProt NPD GO	YL404_YEAST	Uncharacterized protein YLR404W	0.48	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				285
P53938 UniProt NPD GO	YNI0_YEAST	Uncharacterized protein YNL080C	0.48	-	end	4	Membrane; multi-pass membrane protein (Potential)				366
P53871 UniProt NPD GO	YNT1_YEAST	Uncharacterized protein YNL191W	0.48	-	mit	0		cytoplasm [IDA]			357
Q99395 UniProt NPD GO	YP229_YEAST	Uncharacterized protein YPL229W	0.48	-	nuc	0	Cytoplasm	cytoplasm [IDA]			206
P51573 UniProt NPD GO	UPAS_RAT	Urokinase plasminogen activator surface receptor, secreted form precursor (uPAR) (U-PAR) (CD87 antig ...	0.48	-	exc	0	Secreted protein (Probable)				220
Q9UPU3 UniProt NPD GO	SORC3_HUMAN	VPS10 domain-containing receptor SorCS3 precursor	0.48	-	nuc	1	Membrane; single-pass type I membrane protein	membrane [NAS]	606285		1222
Q40272 UniProt NPD GO	VATE_MESCR	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.48	-	nuc	0					226
P48016 UniProt NPD GO	ATH1_YEAST	Vacuolar acid trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose gluco ...	0.48	-	nuc	1 *	Vacuole. Lysosome-like vacuoles (Potential)	cell wall (sensu Fungi) [IDA] periplasmic space (sensu Fungi) [IDA] vacuole (sensu Fungi) [IMP]			1211
P40547 UniProt NPD GO	VID28_YEAST	Vacuolar import and degradation protein 28 (Glucose-induced degradation protein 5)	0.48	-	cyt	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			921
O74925 UniProt NPD GO	PEP3_SCHPO	Vacuolar membrane protein pep3 (Vacuolar protein sorting 18)	0.48	-	mit	0	Vacuole; vacuolar membrane; peripheral membrane protein; cytoplasmic side (By similarity)				900
Q6DDF4 UniProt NPD GO	VPS36_XENLA	Vacuolar protein sorting protein 36	0.48	-	cyt	0	Cytoplasm (By similarity)				388
Q9NRW7 UniProt NPD GO	VPS45_HUMAN	Vacuolar protein sorting-associated protein 45 (h-VPS45) (hlVps45)	0.48	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity). Endosome; endosomal me ...	Golgi-associated vesicle [TAS] lysosome [TAS]			570
P97390 UniProt NPD GO	VPS45_MOUSE	Vacuolar protein sorting-associated protein 45 (mVps45)	0.48	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein. Endosome; endosomal membrane; peripher ...				570
Q6FW96 UniProt NPD GO	SNF7_CANGA	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.48	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				228
P26327 UniProt NPD GO	VSI2_TRYBB	Variant surface glycoprotein ILTAT 1.22 precursor (VSG)	0.48	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				479
Q3HXY2 UniProt NPD GO	NGFV2_PSEAU	Venom nerve growth factor 2 precursor (vNGF-2)	0.48	-	exc	0	Secreted protein				242
Q90W38 UniProt NPD GO	NGFV_BOTJR	Venom nerve growth factor precursor (vNGF) (Bj-NGF)	0.48	-	exc	0	Secreted protein				241
P53340 UniProt NPD GO	YG62_YEAST	Very hypothetical protein YGR291C	0.48	-	nuc	0					73
Q64727 UniProt NPD GO	VINC_MOUSE	Vinculin (Metavinculin)	0.48	-	nuc	0	Cytoskeleton (By similarity). Cell membrane; cell-cell junction; adherens junction; cytoplasmic side ...	adherens junction [IDA] costamere [IDA] focal adhesion [IDA] intercellular junction [IDA]			1065
P22985 UniProt NPD GO	XDH_RAT	Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD); Xanthine oxidas ...	0.48	-	cyt	0	Peroxisome			1WYG	1330
Q8VDA5 UniProt NPD GO	ZBP1_RAT	Z-DNA-binding protein 1 (Tumor stroma and activated macrophage protein DLM-1)	0.48	-	nuc	0					409
Q5R7S6 UniProt NPD GO	Z20D3_PONPY	Zinc finger A20 domain-containing protein 3	0.48	-	nuc	0					208
Q9UNY5 UniProt NPD GO	ZN232_HUMAN	Zinc finger protein 232 (Zinc finger and SCAN domain-containing protein 11)	0.48	-	nuc	0	Nucleus				417
Q14588 UniProt NPD GO	ZN234_HUMAN	Zinc finger protein 234 (Zinc finger protein HZF4)	0.48	-	nuc	0	Nucleus (Probable)		604750		700
Q9GZX5 UniProt NPD GO	ZN350_HUMAN	Zinc finger protein 350 (Zinc-finger protein ZBRK1) (Zinc finger and BRCA1-interacting protein with ...	0.48	-	nuc	0	Nucleus. Associated with the nuclear matrix		605422		532
Q9NWS9 UniProt NPD GO	ZN446_HUMAN	Zinc finger protein 446	0.48	-	nuc	0	Nucleus (Potential)				450
Q6ZR52 UniProt NPD GO	ZN493_HUMAN	Zinc finger protein 493	0.48	-	nuc	0	Nucleus (Potential)				646
Q8NEK5 UniProt NPD GO	ZN548_HUMAN	Zinc finger protein 548	0.48	-	nuc	0	Nucleus (Probable)				533
Q8NEP9 UniProt NPD GO	ZN555_HUMAN	Zinc finger protein 555	0.48	-	nuc	0	Nucleus (Probable)				628

You are viewing entries 26651 to 26700 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.