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
Q6PB44 UniProt NPD GO	PTN23_MOUSE	Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48)	0.60	-	nuc	0	Cytoplasmic vesicle (By similarity)				1692
O88902 UniProt NPD GO	PTN23_RAT	Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) (His-domain-containing protein tyros ...	0.60	-	nuc	0	Cytoplasmic vesicle				1499
Q9FMU5 UniProt NPD GO	UTP18_ARATH	U3 small nucleolar RNA-associated protein 18 homolog	0.60	-	nuc	0	Nucleus; nucleolus (By similarity)				546
P32899 UniProt NPD GO	IMP3_YEAST	U3 small nucleolar ribonucleoprotein protein IMP3 (U3 snoRNP protein IMP3)	0.60	-	nuc	0	Nucleus; nucleolus	small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [IDA]			183
Q6P5E4 UniProt NPD GO	UGGG1_MOUSE	UDP-glucose:glycoprotein glucosyltransferase 1 precursor (EC 2.4.1.-) (UDP-glucose ceramide glucosyl ...	0.60	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity). Endoplasmic reticulum-Golgi inte ...	endoplasmic reticulum lumen [ISS] ER-Golgi intermediate compartment [ISS]			1527
Q68FT1 UniProt NPD GO	COQ9_RAT	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.60	-	nuc	0	Mitochondrion (By similarity)				312
Q6DG43 UniProt NPD GO	UBTD2_BRARE	Ubiquitin domain-containing protein 2	0.60	-	nuc	0	Cytoplasm (By similarity)				240
Q91W82 UniProt NPD GO	UB2E2_MOUSE	Ubiquitin-conjugating enzyme E2 E2 (EC 6.3.2.19) (Ubiquitin-protein ligase E2) (Ubiquitin carrier pr ...	0.60	-	nuc	0					201
Q96LR5 UniProt NPD GO	UB2E2_HUMAN	Ubiquitin-conjugating enzyme E2 E2 (EC 6.3.2.19) (Ubiquitin-protein ligase E2) (Ubiquitin carrier pr ...	0.60	-	nuc	0			602163	1Y6L	201
Q96BY7 UniProt NPD GO	CN103_HUMAN	Uncharacterized protein C14orf103	0.60	-	nuc	0					909
Q4R7D5 UniProt NPD GO	CO033_MACFA	Uncharacterized protein C15orf33 homolog	0.60	-	nuc	0					392
P38289 UniProt NPD GO	YB13_YEAST	Uncharacterized protein YBR163W	0.60	-	nuc	0		mitochondrion [IDA]			585
P25352 UniProt NPD GO	YCR5_YEAST	Uncharacterized protein YCR025C	0.60	-	nuc	0					136
Q03205 UniProt NPD GO	YD042_YEAST	Uncharacterized protein YDR042C	0.60	-	nuc	0					200
P40559 UniProt NPD GO	YIA2_YEAST	Uncharacterized protein YIL002C (EC 3.1.3.-)	0.60	+	nuc	0		membrane fraction [IDA]			946
P53899 UniProt NPD GO	YNP5_YEAST	Uncharacterized protein YNL155W	0.60	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			274
P53146 UniProt NPD GO	USE1_YEAST	Unconventional SNARE in the endoplasmic reticulum protein 1 (SNARE-like tail-anchored protein 1)	0.60	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	endoplasmic reticulum [IDA]			245
Q8VI51 UniProt NPD GO	SORC3_MOUSE	VPS10 domain-containing receptor SorCS3 precursor	0.60	-	nuc	1	Membrane; single-pass type I membrane protein				1219
Q9XZH6 UniProt NPD GO	VATG_DROME	Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G subunit) ...	0.60	-	nuc	0					117
Q5SPW0 UniProt NPD GO	VPS54_MOUSE	Vacuolar protein sorting protein 54 (Tumor antigen SLP-8p homolog)	0.60	-	nuc	0					977
Q9GKR0 UniProt NPD GO	VEGFA_HORSE	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.60	-	exc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				190
P49767 UniProt NPD GO	VEGFC_HUMAN	Vascular endothelial growth factor C precursor (VEGF-C) (Vascular endothelial growth factor-related ...	0.60	-	nuc	0	Secreted protein		601528		419
Q9P7G5 UniProt NPD GO	BOS1_SCHPO	Vesicular transport protein bos1	0.60	-	nuc	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein (By similarity). Secretor ...				235
O46037 UniProt NPD GO	VINC_DROME	Vinculin	0.60	-	nuc	0	Cytoskeleton (By similarity). Cell membrane; cell-cell junction; adherens junction; cytoplasmic side ...				961
Q28278 UniProt NPD GO	PROC_CANFA	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.60	-	mit	0					456
Q8VIC6 UniProt NPD GO	VN1A1_MOUSE	Vomeronasal type-1 receptor A1 (Vomeronasal type-1 receptor A8) (Pheromone receptor 1) (mV1R1)	0.60	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				319
O94967 UniProt NPD GO	WDR47_HUMAN	WD repeat protein 47	0.60	-	nuc	0					919
Q9Y4E6 UniProt NPD GO	WDR7_HUMAN	WD repeat protein 7 (TGF-beta resistance-associated protein TRAG) (Rabconnectin-3 beta)	0.60	-	mit	0					1490
O14170 UniProt NPD GO	POP2_SCHPO	WD repeat protein pop2 (Proteolysis factor sud1)	0.60	-	nuc	0	Cytoplasm. Nucleus	nuclear SCF ubiquitin ligase complex [IDA]			703
Q8GY25 UniProt NPD GO	WOX12_ARATH	WUSCHEL-related homeobox 12	0.60	-	nuc	0	Nucleus (By similarity)				268
Q9HCJ5 UniProt NPD GO	ZSWM6_HUMAN	Zinc finger SWIM domain-containing protein 6 (Fragment)	0.60	-	cyt	0					743
O62836 UniProt NPD GO	ZFX_BOVIN	Zinc finger X-chromosomal protein	0.60	+	nuc	0	Nucleus				800
Q6B4Z5 UniProt NPD GO	ZFY_PANTR	Zinc finger Y-chromosomal protein	0.60	+	nuc	0	Nucleus				801
P23607 UniProt NPD GO	ZFA_MOUSE	Zinc finger autosomal protein	0.60	+	nuc	0	Nucleus				742
Q5RAU9 UniProt NPD GO	ZN131_PONPY	Zinc finger protein 131	0.60	-	cyt	0	Nucleus (Potential)				589
Q15776 UniProt NPD GO	ZN192_HUMAN	Zinc finger protein 192 (LD5-1)	0.60	-	nuc	0	Nucleus (Potential)		602240		578
O75437 UniProt NPD GO	ZN254_HUMAN	Zinc finger protein 254 (Bone marrow zinc finger 5) (BMZF-5) (Hematopoietic cell-derived zinc finger ...	0.60	-	nuc	0	Nucleus (Probable)		604768		353
Q9P2F9 UniProt NPD GO	ZN319_HUMAN	Zinc finger protein 319	0.60	-	nuc	0	Nucleus (Probable)				582
Q96SR6 UniProt NPD GO	ZN382_HUMAN	Zinc finger protein 382 (KRAB/Zinc finger suppressor protein 1) (KS1)	0.60	+	nuc	0	Nucleus (Probable)		609516		548
Q96IQ9 UniProt NPD GO	ZN414_HUMAN	Zinc finger protein 414	0.60	-	nuc	0	Nucleus (Probable)				312
Q6AXX3 UniProt NPD GO	ZN659_RAT	Zinc finger protein 659	0.60	-	nuc	0	Nucleus (Potential)				395
Q8NEM1 UniProt NPD GO	ZN680_HUMAN	Zinc finger protein 680	0.60	-	nuc	0	Nucleus (Probable)				530
Q8N9L1 UniProt NPD GO	ZIC4_HUMAN	Zinc finger protein ZIC 4 (Zinc finger protein of the cerebellum 4)	0.60	-	nuc	0	Nucleus (By similarity)		608948		334
Q5R670 UniProt NPD GO	ZKSC1_PONPY	Zinc finger with KRAB and SCAN domain-containing protein 1	0.60	-	nuc	0	Nucleus (Potential)				563
P81900 UniProt NPD GO	KAPR2_DROME	cAMP-dependent protein kinase type II regulatory subunit	0.60	+	mit	0	Cytoplasm	cytoplasm [IDA]			377
Q13237 UniProt NPD GO	KGP2_HUMAN	cGMP-dependent protein kinase 2 (EC 2.7.11.12) (CGK 2) (cGKII) (Type II cGMP-dependent protein kinas ...	0.60	-	cyt	0			601591		762
Q9D7B1 UniProt NPD GO	DUS2L_MOUSE	tRNA-dihydrouridine synthase 2-like (EC 1.-.-.-)	0.60	-	cyt	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Mainly at the endoplasmic reticulu ...			1WHN	493
Q04952 UniProt NPD GO	GLS3_YEAST	1,3-beta-glucan synthase component FKS3 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase)	0.59	-	end	18	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			1785
Q43309 UniProt NPD GO	1A14_ARATH	1-aminocyclopropane-1-carboxylate synthase 4 (EC 4.4.1.14) (ACC synthase 4) (S-adenosyl-L-methionine ...	0.59	-	nuc	0					474
P01089 UniProt NPD GO	2SS_RICCO	2S albumin precursor (Allergen Ric c 1/3) [Contains: Allergen Ric c 3 small chain (4.7 kDa napin-lik ...	0.59	-	exc	1 *				1PSY	258

You are viewing entries 19351 to 19400 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.