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
Q92830 UniProt NPD GO	GCNL2_HUMAN	General control of amino acid synthesis protein 5-like 2 (EC 2.3.1.48) (Histone acetyltransferase GC ...	0.70	-	nuc	0	Nucleus		602301	1Z4R	837
P97494 UniProt NPD GO	GSH1_MOUSE	Glutamate--cysteine ligase catalytic subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma ...	0.70	+	nuc	0					636
Q02979 UniProt NPD GO	GDE1_YEAST	Glycerophosphodiester phosphodiesterase GDE1 (EC 3.1.4.46)	0.70	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1223
Q5RBL6 UniProt NPD GO	GOSR1_PONPY	Golgi SNAP receptor complex member 1	0.70	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity). Enriched on v ...				248
O95249 UniProt NPD GO	GOSR1_HUMAN	Golgi SNAP receptor complex member 1 (28 kDa Golgi SNARE protein) (28 kDa cis-Golgi SNARE p28) (GOS- ...	0.70	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity). Enriched on v ...		604026		250
Q14451 UniProt NPD GO	GRB7_HUMAN	Growth factor receptor-bound protein 7 (GRB7 adapter protein) (Epidermal growth factor receptor GRB- ...	0.70	-	nuc	0			601522	1WGR	532
Q7Z5L2 UniProt NPD GO	GIDRP_HUMAN	Growth inhibition and differentiation-related protein 88 (Putative mitochondrial space protein 32.1) ...	0.70	-	nuc	0					792
P28868 UniProt NPD GO	GPA1_CANAL	Guanine nucleotide-binding protein subunit alpha	0.70	-	cyt	0					428
Q9NQ75 UniProt NPD GO	CT032_HUMAN	HEF-like protein	0.70	-	nuc	0				2CRE	786
P62684 UniProt NPD GO	GAK5_HUMAN	HERV-K_19p13.11 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K113 Gag protein) [Contai ...	0.70	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
P87889 UniProt NPD GO	GAK10_HUMAN	HERV-K_5q33.3 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K10 Gag protein) (HERV-K107 ...	0.70	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system)				665
P63133 UniProt NPD GO	POK6_HUMAN	HERV-K_8p23.1 provirus ancestral Pol protein (HERV-K115 Pol protein) [Includes: Reverse transcriptas ...	0.70	-	nuc	0					956
Q9TSZ2 UniProt NPD GO	HEY1_CANFA	Hairy/enhancer-of-split related with YRPW motif 1 (Hairy and enhancer of split-related protein 1) (H ...	0.70	+	nuc	0	Nucleus (By similarity)				304
Q7TN16 UniProt NPD GO	HHIP_MOUSE	Hedgehog-interacting protein precursor (HHIP) (HIP)	0.70	+	exc	0	Cell membrane; peripheral membrane protein. Secreted protein. The last 22 C-terminal amino acids may ...	cell surface [IDA] integral to plasma membrane [IDA]			700
Q800H9 UniProt NPD GO	H6ST2_BRARE	Heparan-sulfate 6-O-sulfotransferase 2 (EC 2.8.2.-) (HS6ST-2)	0.70	+	end	1 *	Membrane; single-pass type II membrane protein (Potential)				468
Q923W4 UniProt NPD GO	HDGR3_RAT	Hepatoma-derived growth factor-related protein 3 (HRP-3)	0.70	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			202
Q969F9 UniProt NPD GO	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein	0.70	-	nuc	0	Cytoplasm (By similarity)		606118		1004
Q4WHG1 UniProt NPD GO	ESA1_ASPFU	Histone acetyltransferase esa1 (EC 2.3.1.48)	0.70	-	cyt	0	Nucleus (By similarity)				483
P32479 UniProt NPD GO	HIR1_YEAST	Histone transcription regulator 1	0.70	-	nuc	0	Nucleus	chromosome, pericentric region [IDA] nucleus [IPI]			840
P34470 UniProt NPD GO	HCP3_CAEEL	Holocentric chromosome-binding protein 3	0.70	-	nuc	0	Nucleus	condensed chromosome, pericentric region [IDA] nucleus [IDA]			288
Q96QS3 UniProt NPD GO	ARX_HUMAN	Homeobox protein ARX (Aristaless-related homeobox)	0.70	+	nuc	0	Nucleus (By similarity)		309510		562
P10178 UniProt NPD GO	HMB3_TRIGR	Homeobox protein HB3 (Fragment)	0.70	+	nuc	0	Nucleus (Probable)				108
Q8AWZ2 UniProt NPD GO	HXA3A_BRARE	Homeobox protein Hox-A3a	0.70	+	nuc	0	Nucleus (By similarity)				410
P81192 UniProt NPD GO	HXA4_LINSA	Homeobox protein Hox-A4 (LsHox 4) (Fragment)	0.70	+	nuc	0	Nucleus (By similarity)				80
P32043 UniProt NPD GO	HXC5_MOUSE	Homeobox protein Hox-C5 (Hox-3.4) (Hox-6.2)	0.70	+	nuc	0	Nucleus				222
Q8TAU0 UniProt NPD GO	NKX23_HUMAN	Homeobox protein Nkx-2.3 (Homeobox protein NKX-2.3) (Homeobox protein NK-2 homolog C)	0.70	+	nuc	0	Nucleus (By similarity)		606727		364
Q9EQM3 UniProt NPD GO	NKX24_MOUSE	Homeobox protein Nkx-2.4 (Homeobox protein NKX2.4) (Homeobox protein NK-2 homolog D)	0.70	-	nuc	0	Nucleus (By similarity)				354
O73916 UniProt NPD GO	SIX3_ORYLA	Homeobox protein SIX3 (Sine oculis homeobox homolog 3)	0.70	-	nuc	0	Nucleus (By similarity)				272
Q26602 UniProt NPD GO	SMOX3_SCHMA	Homeobox protein SMOX-3 (Fragment)	0.70	+	mit	0	Nucleus (By similarity)				288
Q22812 UniProt NPD GO	HM39_CAEEL	Homeobox protein ceh-39	0.70	-	nuc	0	Nucleus (Potential)				399
Q8MJI9 UniProt NPD GO	PROP1_BOVIN	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.70	+	nuc	0	Nucleus (By similarity)				226
Q3LU39 UniProt NPD GO	PROP1_GORGO	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.70	+	nuc	0	Nucleus (By similarity)				225
Q99L47 UniProt NPD GO	F10A1_MOUSE	Hsc70-interacting protein (Hip) (Protein ST13 homolog) (Protein FAM10A1)	0.70	-	nuc	0	Cytoplasm (By similarity)				371
Q61081 UniProt NPD GO	CDC37_MOUSE	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (p50Cdc37)	0.70	-	cyt	0	Cytoplasm				379
Q9JLZ6 UniProt NPD GO	HIC2_MOUSE	Hypermethylated in cancer 2 protein (Hic-2)	0.70	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			672
P34241 UniProt NPD GO	YKB4_YEAST	Hypothetical 203.3 kDa protein in PUT3-ARC19 intergenic region	0.70	-	end	0		nucleolus [IDA]			1764
P49540 UniProt NPD GO	YCF45_ODOSI	Hypothetical 51.9 kDa protein ycf45 (ORF455)	0.70	-	nuc	0	Plastid; chloroplast				455
P53129 UniProt NPD GO	YGM4_YEAST	Hypothetical 73.5 kDa protein in MET13-RPS2 intergenic region	0.70	-	nuc	0		cytosol [IDA] vacuolar membrane (sensu Fungi) [IDA]			644
Q10422 UniProt NPD GO	YDC1_SCHPO	Hypothetical RNA-binding protein C25G10.01 in chromosome I	0.70	+	nuc	0					297
Q9USY0 UniProt NPD GO	YOW6_SCHPO	Hypothetical UPF0300 protein C1861.06c in chromosome II	0.70	-	nuc	0					433
O94459 UniProt NPD GO	YFFI_SCHPO	Hypothetical protein C1687.18c in chromosome I	0.70	-	nuc	0					559
O13771 UniProt NPD GO	YE99_SCHPO	Hypothetical protein C17A5.09c in chromosome I	0.70	-	nuc	0					310
Q9UT42 UniProt NPD GO	YIPJ_SCHPO	Hypothetical protein C343.19 in chromosome I	0.70	-	nuc	0					624
P87129 UniProt NPD GO	YDLF_SCHPO	Hypothetical protein C3A12.15 in chromosome I	0.70	-	nuc	0					756
Q09288 UniProt NPD GO	YQK4_CAEEL	Hypothetical protein C56G2.4 precursor	0.70	-	exc	0					538
O14208 UniProt NPD GO	YDT3_SCHPO	Hypothetical protein C6B12.03c in chromosome I	0.70	+	cyt	0					302
P34474 UniProt NPD GO	YMH7_CAEEL	Hypothetical protein F58A4.7 in chromosome III	0.70	-	nuc	0	Nucleus (Potential)				431
P34491 UniProt NPD GO	YMM3_CAEEL	Hypothetical protein K01B6.3	0.70	+	end	4					410
P05524 UniProt NPD GO	FGF3_MOUSE	INT-2 proto-oncogene protein precursor (Fibroblast growth factor 3) (FGF-3) (HBGF-3)	0.70	+	nuc	0	Isoform 1: Nucleus. Isoform 2: Endoplasmic reticulum. Golgi apparatus				245
O35857 UniProt NPD GO	TIM44_MOUSE	Import inner membrane translocase subunit TIM44, mitochondrial precursor	0.70	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			452

You are viewing entries 13751 to 13800 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.