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
Q9NYU2 UniProt NPD GO	UGGG1_HUMAN	UDP-glucose:glycoprotein glucosyltransferase 1 precursor (EC 2.4.1.-) (UDP-glucose ceramide glucosyl ...	0.51	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Endoplasmic reticulum-Golgi intermediate compart ...	endoplasmic reticulum [IDA] ER-Golgi intermediate compartment [ISS]	605897		1531
Q9UHD9 UniProt NPD GO	UBQL2_HUMAN	Ubiquilin-2 (Protein linking IAP with cytoskeleton 2) (PLIC-2) (hPLIC-2) (Ubiquitin-like product Cha ...	0.51	-	nuc	0	Cytoplasm. Where it colocalizes with the proteasome. Associated with fibers in mitotic cells. Nucleu ...		300264	1J8C	624
Q9NRR5 UniProt NPD GO	UBQL4_HUMAN	Ubiquilin-4 (Ataxin-1 ubiquitin-like-interacting protein A1U)	0.51	-	nuc	0	Nucleus. Cytoplasm. Endoplasmic reticulum (Probable). May associate with the endoplasmic reticulum	cytoplasm [IDA] cytosol [ISS] endoplasmic reticulum membrane [ISS] nucleus [IDA]	605440		601
O57429 UniProt NPD GO	UBP2_CHICK	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin-specific ...	0.51	-	mit	0					357
Q29504 UniProt NPD GO	UBE1_RABIT	Ubiquitin-activating enzyme E1	0.51	-	nuc	0					1058
Q02053 UniProt NPD GO	UBE1_MOUSE	Ubiquitin-activating enzyme E1 1	0.51	-	nuc	0				1Z7L	1058
Q32P99 UniProt NPD GO	UBE2B_BOVIN	Ubiquitin-conjugating enzyme E2 B (EC 6.3.2.19) (Ubiquitin-protein ligase B) (Ubiquitin carrier prot ...	0.51	-	nuc	0	Cell membrane (By similarity). Nucleus (By similarity). In peripheral neurons, expressed both at the ...				152
P63148 UniProt NPD GO	UBE2B_RABIT	Ubiquitin-conjugating enzyme E2 B (EC 6.3.2.19) (Ubiquitin-protein ligase B) (Ubiquitin carrier prot ...	0.51	-	nuc	0	Cell membrane (By similarity). Nucleus (By similarity). In peripheral neurons, expressed both at the ...				152
P63149 UniProt NPD GO	UBE2B_RAT	Ubiquitin-conjugating enzyme E2 B (EC 6.3.2.19) (Ubiquitin-protein ligase B) (Ubiquitin carrier prot ...	0.51	-	nuc	0	Cell membrane. Nucleus. In peripheral neurons, expressed both at the plasma membrane and in nuclei				152
P63147 UniProt NPD GO	UBE2B_MOUSE	Ubiquitin-conjugating enzyme E2 B (EC 6.3.2.19) (Ubiquitin-protein ligase B) (Ubiquitin carrier prot ...	0.51	-	nuc	0	Cell membrane (By similarity). Nucleus (By similarity). In peripheral neurons, expressed both at the ...	chromatin [IDA]			152
P63146 UniProt NPD GO	UBE2B_HUMAN	Ubiquitin-conjugating enzyme E2 B (EC 6.3.2.19) (Ubiquitin-protein ligase B) (Ubiquitin carrier prot ...	0.51	-	nuc	0	Cell membrane (By similarity). Nucleus (By similarity). In peripheral neurons, expressed both at the ...		179095	1NXA	152
Q757D9 UniProt NPD GO	BRE1_ASHGO	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.51	-	nuc	0	Nucleus (By similarity)				643
P53857 UniProt NPD GO	YNX4_YEAST	Uncharacterized globin-like protein YNL234W	0.51	-	nuc	0		cytoplasm [IDA]			426
P38888 UniProt NPD GO	YH04_YEAST	Uncharacterized glycosyl hydrolase YHR204W precursor (EC 3.2.1.-)	0.51	+	exc	0		endoplasmic reticulum [IDA]			796
P40530 UniProt NPD GO	YIE2_YEAST	Uncharacterized kinase YIL042C (EC 2.7.11.-)	0.51	-	mit	0					394
Q9P2W6 UniProt NPD GO	CK021_HUMAN	Uncharacterized protein C11orf21	0.51	+	nuc	0	Cytoplasm				132
Q5BJY3 UniProt NPD GO	CR037_RAT	Uncharacterized protein C18orf37 homolog	0.51	+	nuc	0					191
Q9BWL3 UniProt NPD GO	CA043_HUMAN	Uncharacterized protein C1orf43 (Hepatitis C virus NS5A-transactivated protein 4) (Protein NICE-3) ( ...	0.51	-	nuc	1 *					253
O13929 UniProt NPD GO	YF69_SCHPO	Uncharacterized protein C23C4.09c	0.51	-	nuc	0					131
Q9VCF0 UniProt NPD GO	Y5902_DROME	Uncharacterized protein CG5902	0.51	-	nuc	0					243
Q03983 UniProt NPD GO	YD179_YEAST	Uncharacterized protein YDR179W-A	0.51	-	nuc	0					463
P40038 UniProt NPD GO	YEO9_YEAST	Uncharacterized protein YER059W	0.51	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			420
P40053 UniProt NPD GO	YER0_YEAST	Uncharacterized protein YER080W	0.51	-	mit	0		mitochondrion [IDA]			627
P53172 UniProt NPD GO	YGF6_YEAST	Uncharacterized protein YGL056C	0.51	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			527
P53292 UniProt NPD GO	YG3V_YEAST	Uncharacterized protein YGR165W	0.51	-	mit	0		mitochondrial small ribosomal subunit [IPI]			345
P34240 UniProt NPD GO	YKR5_YEAST	Uncharacterized protein YKL175W	0.51	-	mit	8 *		vacuolar membrane [IDA]			503
Q07927 UniProt NPD GO	YL012_YEAST	Uncharacterized protein YLR012C	0.51	-	cyt	0					99
Q3E846 UniProt NPD GO	YM244_YEAST	Uncharacterized protein YMR244C-A	0.51	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			104
Q02864 UniProt NPD GO	YP071_YEAST	Uncharacterized protein YPL071C	0.51	+	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			156
P25022 UniProt NPD GO	RAG2_CHICK	V(D)J recombination-activating protein 2 (RAG-2)	0.51	-	nuc	0	Nucleus				528
P87220 UniProt NPD GO	VATD_CANAL	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.51	-	cyt	0					267
P31402 UniProt NPD GO	VATE_MANSE	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.51	-	nuc	0					226
Q3HXX6 UniProt NPD GO	NGFV3_TROCA	Venom nerve growth factor 3 precursor (vNGF-3)	0.51	-	exc	0	Secreted protein				243
P34128 UniProt NPD GO	NGFV_BUNMU	Venom nerve growth factor precursor (v-NGF)	0.51	-	exc	0	Secreted protein				243
Q5SQQ9 UniProt NPD GO	VAX1_HUMAN	Ventral anterior homeobox 1	0.51	+	nuc	0	Nucleus (By similarity)		604294		334
P98165 UniProt NPD GO	VLDLR_CHICK	Very low-density lipoprotein receptor precursor (VLDL receptor) (VLDL-R) (Vitellogenin receptor) (VT ...	0.51	-	exc	1	Membrane; single-pass type I membrane protein				863
Q92155 UniProt NPD GO	VIME_CYPCA	Vimentin	0.51	-	nuc	0					455
Q3MHN5 UniProt NPD GO	VTDB_BOVIN	Vitamin D-binding protein precursor (DBP) (Group-specific component) (Gc-globulin) (VDB)	0.51	-	exc	0	Secreted protein				474
Q90508 UniProt NPD GO	VIT1_FUNHE	Vitellogenin-1 precursor (Vitellogenin I) (VTG I) [Contains: Lipovitellin-1 (LV1); Phosvitin (PV); L ...	0.51	-	nuc	0					1704
Q91025 UniProt NPD GO	VIT3_CHICK	Vitellogenin-3 precursor (Vitellogenin III) (Minor vitellogenin) (VYGIII) [Contains: Phosvitin (PV)] ...	0.51	-	exc	0					347
Q16927 UniProt NPD GO	VIT1_AEDAE	Vitellogenin-A1 precursor (VG) (PVG1) [Contains: Vitellin light chain (VL); Vitellin heavy chain (VH ...	0.51	-	nuc	0					2148
Q9EQ52 UniProt NPD GO	VN1A3_MOUSE	Vomeronasal type-1 receptor A3 (Vomeronasal type-1 receptor A6)	0.51	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				302
Q9EQ51 UniProt NPD GO	VN1A4_MOUSE	Vomeronasal type-1 receptor A4 (Vomeronasal type-1 receptor A7)	0.51	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q810W9 UniProt NPD GO	WHRN_RAT	Whirlin (CASK-interacting protein CIP98)	0.51	-	nuc	0	Cytoplasm. Detected at the level of stereocilia in inner hair cells and in outer hair cells in the c ...				920
Q8RWI9 UniProt NPD GO	WBC15_ARATH	White-brown complex homolog protein 15 (White-brown complex homolog protein 22)	0.51	-	end	7	Membrane; multi-pass membrane protein (By similarity)				691
Q09020 UniProt NPD GO	PR4_PHAVU	Wound-induced basic protein	0.51	-	nuc	0					47
Q9EPI1 UniProt NPD GO	XYLT1_RAT	Xylosyltransferase 1 (EC 2.4.2.26) (Xylosyltransferase I) (Peptide O-xylosyltransferase 1) (Fragment ...	0.51	-	nuc	0	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				821
Q9BYJ9 UniProt NPD GO	YTHD1_HUMAN	YTH domain protein 1 (Dermatomyositis associated with cancer putative autoantigen 1) (DACA-1)	0.51	-	nuc	0					559
Q8BYK6 UniProt NPD GO	YTHD3_MOUSE	YTH domain protein 3	0.51	-	nuc	0					585
Q6DGF4 UniProt NPD GO	Z20D3_RAT	Zinc finger A20 domain-containing protein 3	0.51	-	nuc	0					223

You are viewing entries 24701 to 24750 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.