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
Q9D0D5 UniProt NPD GO	T2EA_MOUSE	Transcription initiation factor IIE subunit alpha (TFIIE-alpha) (General transcription factor IIE 56 ...	0.40	-	cyt	0	Nucleus				440
Q9XZT7 UniProt NPD GO	TAFAB_DROME	Transcription initiation factor TFIID subunit 10b (Transcription initiation factor TFIID 16 kDa subu ...	0.40	-	nuc	0	Cytoplasm. Nucleus	transcription factor TFIID complex [IDA]			146
P69744 UniProt NPD GO	TRPV5_MOUSE	Transient receptor potential cation channel subfamily V member 5 (TrpV5) (osm-9-like TRP channel 3) ...	0.40	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein. Colocalized with S100A10 and ANAX2 ...	apical plasma membrane [IDA] integral to plasma membrane [ISS]			723
P57997 UniProt NPD GO	IF2C_PHAVU	Translation initiation factor IF-2, chloroplast precursor (PvIF2cp)	0.40	-	mit	0	Plastid; chloroplast				1012
P36177 UniProt NPD GO	IF3C_EUGGR	Translation initiation factor IF-3, chloroplast precursor (IF-3chl)	0.40	-	end	2 *	Plastid; chloroplast				538
Q32PR0 UniProt NPD GO	T55BA_BRARE	Transmembrane protein 55B-A (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase ...	0.40	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				270
P36096 UniProt NPD GO	TUL1_YEAST	Transmembrane ubiquitin ligase 1 (EC 6.3.2.-)	0.40	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [IDA]			758
Q99LG2 UniProt NPD GO	TNPO2_MOUSE	Transportin-2 (Karyopherin beta-2b)	0.40	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				887
P14380 UniProt NPD GO	YTX1_XENLA	Transposon TX1 hypothetical 82 kDa protein (ORF 1)	0.40	+	nuc	0					775
Q58DK8 UniProt NPD GO	TRI38_BOVIN	Tripartite motif-containing protein 38	0.40	-	cyt	0					460
Q96BQ3 UniProt NPD GO	TRI43_HUMAN	Tripartite motif-containing protein 43	0.40	-	cyt	0					446
Q9C035 UniProt NPD GO	TRIM5_HUMAN	Tripartite motif-containing protein 5 (EC 6.3.2.-) (RING finger protein 88)	0.40	-	cyt	0	Cytoplasm. Cytoplasmic bodies				493
P70566 UniProt NPD GO	TMOD2_RAT	Tropomodulin-2 (Neuronal tropomodulin) (N-Tmod)	0.40	-	nuc	0					351
Q9NAS5 UniProt NPD GO	TPM_ANISI	Tropomyosin (Allergen Ani s 3)	0.40	-	nuc	0					284
O18416 UniProt NPD GO	TPM_DERPT	Tropomyosin (Allergen Der p 10)	0.40	-	nuc	0					284
O44119 UniProt NPD GO	TPM_HOMAM	Tropomyosin (Allergen Hom a 1)	0.40	-	nuc	0					284
P41114 UniProt NPD GO	TPM1_PODCA	Tropomyosin 1	0.40	-	nuc	0					242
Q6X2E2 UniProt NPD GO	DMAW1_ACRCO	Tryptophan dimethylallyltransferase 1 (EC 2.5.1.34) (DMATS 1) (All-trans-hexaprenyl-diphosphate synt ...	0.40	-	cyt	0					448
P20364 UniProt NPD GO	TBB1_DAUCA	Tubulin beta-1 chain (Beta-1 tubulin) (Fragment)	0.40	-	cyt	0					315
Q9Y2W6 UniProt NPD GO	TDRKH_HUMAN	Tudor and KH domain-containing protein	0.40	-	nuc	1 *			609501		606
Q9R1R4 UniProt NPD GO	TDRD7_RAT	Tudor domain-containing protein 7 (Tudor repeat associator with PCTAIRE 2) (Trap)	0.40	-	cyt	0	Cytoplasm (By similarity). According to Ref.1 localizes preferentially on the periphery of mitochond ...				1113
P20333 UniProt NPD GO	TNR1B_HUMAN	Tumor necrosis factor receptor superfamily member 1B precursor (Tumor necrosis factor receptor 2) (T ...	0.40	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, TBP-II: Secreted protein		191191	1CA9	461
Q9QXE4 UniProt NPD GO	T53I1_MOUSE	Tumor protein p53-inducible nuclear protein 1 (p53-dependent damage-inducible nuclear protein 1) (p5 ...	0.40	-	nuc	0	Nucleus. Isoform 2: Cytoplasm. Isoform 2 is also detected in the cytoplasm	nucleus [IDA]			239
O14683 UniProt NPD GO	P5I11_HUMAN	Tumor protein p53-inducible protein 11 (p53-induced protein 11)	0.40	-	nuc	0					177
Q6LA43 UniProt NPD GO	APRR2_ARATH	Two-component response regulator-like APRR2 (Pseudo-response regulator 2) (TOC2 protein)	0.40	-	nuc	0	Nucleus (Probable)				535
P18898 UniProt NPD GO	CAL1_YEAST	Type-1 proteins geranylgeranyltransferase subunit beta (EC 2.5.1.59) (Type I proteins geranylgeranyl ...	0.40	-	nuc	0		CAAX-protein geranylgeranyltransferase complex [IDA] intracellular [TAS]			376
P54834 UniProt NPD GO	TYRO_CANFA	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.40	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (By similarity)				530
Q27324 UniProt NPD GO	RYK1_DROME	Tyrosine-protein kinase Drl precursor (EC 2.7.10.1) (Protein derailed)	0.40	-	end	1 *		integral to membrane [ISS]			610
Q01887 UniProt NPD GO	RYK_MOUSE	Tyrosine-protein kinase RYK precursor (EC 2.7.10.1) (Kinase VIK) (NYK-R) (Met-related kinase)	0.40	-	end	1	Membrane; single-pass type I membrane protein (Potential)	membrane fraction [IDA] plasma membrane [IDA]			594
Q90687 UniProt NPD GO	PTN11_CHICK	Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) (cSH-PTP2)	0.40	-	mit	0	Cytoplasm (By similarity)				593
P12063 UniProt NPD GO	SYYM_NEUCR	Tyrosyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrRS)	0.40	-	mit	0	Mitochondrion; mitochondrial matrix			1Y42	669
Q5REE0 UniProt NPD GO	UTP15_PONPY	U3 small nucleolar RNA-associated protein 15 homolog	0.40	-	cyt	0	Nucleus; nucleolus (By similarity)				518
Q10212 UniProt NPD GO	YAY4_SCHPO	UPF0103 protein C4H3.04c	0.40	-	nuc	0					309
Q9UTT1 UniProt NPD GO	UBP21_SCHPO	Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) (Ubiquitin thioesterase 21) (Ubiquitin-specif ...	0.40	-	cyt	0	Nucleus	nucleus [IDA]			1129
Q6CUD9 UniProt NPD GO	UBC2_KLULA	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.40	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				164
Q12393 UniProt NPD GO	YL091_YEAST	Uncharacterized mitochondrial protein YLR091W	0.40	-	nuc	0	Mitochondrion	mitochondrion [IDA]			293
Q99K95 UniProt NPD GO	CT043_MOUSE	Uncharacterized protein C20orf43 homolog	0.40	-	nuc	0					307
Q6P7B2 UniProt NPD GO	CB024_RAT	Uncharacterized protein C2orf24 homolog	0.40	-	nuc	0					408
P10356 UniProt NPD GO	YEY2_YEAST	Uncharacterized protein YER152C	0.40	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			443
Q03760 UniProt NPD GO	YMK7_YEAST	Uncharacterized protein YML107C	0.40	+	nuc	0	Nucleus; nuclear membrane; peripheral membrane protein	nuclear pore [IDA]			334
Q04949 UniProt NPD GO	YM8X_YEAST	Uncharacterized protein YMR299C	0.40	-	cyt	0		cytoplasmic dynein complex [IPI] cytoplasmic microtubule [IDA]			312
Q12106 UniProt NPD GO	YO228_YEAST	Uncharacterized protein YOR228C	0.40	-	end	5	Mitochondrion; outer membrane; multi-pass membrane protein (Potential)	mitochondrial outer membrane [IDA] mitochondrion [IDA]			302
P13051 UniProt NPD GO	UNG_HUMAN	Uracil-DNA glycosylase (EC 3.2.2.-) (UDG)	0.40	-	mit	0	Isoform 1: Mitochondrion. Isoform 2: Nucleus	nucleus [NAS]	191525	4SKN	313
P00749 UniProt NPD GO	UROK_HUMAN	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.40	-	exc	0			191840	2FD6	431
P16227 UniProt NPD GO	UROK_PAPCY	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.40	-	exc	0					433
P53853 UniProt NPD GO	VPS75_YEAST	Vacuolar protein sorting protein 75	0.40	-	mit	0	Nucleus	nucleus [IDA]			264
P49765 UniProt NPD GO	VEGFB_HUMAN	Vascular endothelial growth factor B precursor (VEGF-B) (VEGF-related factor) (VRF)	0.40	-	exc	0	Secreted protein. Secreted but remains associated to cells or to the extracellular matrix unless rel ...	extracellular region [NAS]	601398		207
Q7L8A9 UniProt NPD GO	VASH_HUMAN	Vasohibin	0.40	+	nuc	0	Secreted protein (Probable)		609011		365
P08163 UniProt NPD GO	NEUV_BUFJA	Vasotocin-neurophysin VT precursor (VT) [Contains: Hydrin-2 (Hydrin II); Vasotocin; Neurophysin VT; ...	0.40	-	exc	0	Secreted protein				159
Q00808 UniProt NPD GO	HETE1_PODAN	Vegetative incompatibility protein HET-E-1	0.40	-	cyt	0					1356

You are viewing entries 32251 to 32300 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.