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
Q99P96 UniProt NPD GO	HDAC7_RAT	Histone deacetylase 7a (HD7a) (Fragment)	0.87	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In the nucleus, it associates with distinct subn ...	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			238
Q9MA43 UniProt NPD GO	ATX2_ARATH	Histone-lysine N-methyltransferase ATX2 (EC 2.1.1.43) (Trithorax-homolog protein 2) (TRX-homolog pro ...	0.87	+	nuc	0	Nucleus (By similarity)				1193
Q2YDJ8 UniProt NPD GO	SETD8_BOVIN	Histone-lysine N-methyltransferase, H4 lysine-20 specific (EC 2.1.1.43) (Histone H4-K20 methyltransf ...	0.87	-	nuc	0	Nucleus (By similarity). Associates with silent chromatin on euchromatic arms. No association with c ...				352
Q8IX15 UniProt NPD GO	HOMEZ_HUMAN	Homeobox and leucine zipper protein Homez (Homeodomain leucine zipper-containing factor)	0.87	-	nuc	0	Nucleus		608119	1WJH	525
P58304 UniProt NPD GO	CHX10_HUMAN	Homeobox protein CHX10 (Ceh-10 homeodomain-containing homolog)	0.87	+	nuc	0	Nucleus		142993		361
Q9IAL1 UniProt NPD GO	CHX10_CHICK	Homeobox protein Chx10 (Ceh-10 homeodomain-containing homolog)	0.87	+	nuc	0	Nucleus (By similarity)				377
O13074 UniProt NPD GO	HXB4_FUGRU	Homeobox protein Hox-B4 (HOXB-4)	0.87	+	nuc	0	Nucleus				251
Q90469 UniProt NPD GO	HXDAA_BRARE	Homeobox protein Hox-D10a (Hox-D10) (Hox-C10)	0.87	+	nuc	0	Nucleus				343
Q9IA12 UniProt NPD GO	HXD8_HETFR	Homeobox protein Hox-D8	0.87	+	nuc	0	Nucleus (By similarity)				240
P39020 UniProt NPD GO	MEOX2_RAT	Homeobox protein MOX-2 (Growth arrest-specific homeobox)	0.87	+	nuc	0	Nucleus (Potential)				303
Q9H161 UniProt NPD GO	ALX4_HUMAN	Homeobox protein aristaless-like 4	0.87	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]	609597		411
Q9NLC2 UniProt NPD GO	HM24_CAEEL	Homeobox protein ceh-24	0.87	-	nuc	0	Nucleus (By similarity)				299
Q9BL02 UniProt NPD GO	CUT_CAEEL	Homeobox protein cut-like ceh-44 (Homeobox protein 44)	0.87	-	nuc	0	Nucleus (By similarity)				1273
P34326 UniProt NPD GO	HM16_CAEEL	Homeobox protein engrailed-like ceh-16	0.87	+	mit	0	Nucleus				187
Q3LU40 UniProt NPD GO	PROP1_CEBAP	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.87	+	nuc	0	Nucleus (By similarity)				226
P46600 UniProt NPD GO	HAT1_ARATH	Homeobox-leucine zipper protein HAT1 (HD-ZIP protein 1)	0.87	+	nuc	0	Nucleus (Potential)				282
O88904 UniProt NPD GO	HIPK1_MOUSE	Homeodomain-interacting protein kinase 1 (EC 2.7.11.1) (Protein kinase Myak) (Nuclear body-associate ...	0.87	-	nuc	0	Nucleus. Predominantly. Cytoplasm	cytoplasm [IDA] nuclear speck [IDA] nucleus [ISS] PML body [IDA]			1210
Q9WUM7 UniProt NPD GO	HIPK2_MESAU	Homeodomain-interacting protein kinase 2 (EC 2.7.11.1) (Mx-interacting protein kinase) (PKM)	0.87	-	nuc	0	Nucleus. Concentrated in PML/POD/ND10 nuclear bodies				1168
Q9H2X6 UniProt NPD GO	HIPK2_HUMAN	Homeodomain-interacting protein kinase 2 (EC 2.7.11.1) (hHIPk2)	0.87	-	nuc	0	Nucleus. Concentrated in PML/POD/ND10 nuclear bodies. Cytoplasm. Small amounts are cytoplasmic	cytoplasm [ISS] nuclear body [TAS] nucleus [IDA]	606868		1198
O88866 UniProt NPD GO	HUNK_MOUSE	Hormonally up-regulated neu tumor-associated kinase (EC 2.7.11.1) (Serine/threonine-protein kinase M ...	0.87	-	nuc	0					714
P54256 UniProt NPD GO	HAP1_RAT	Huntingtin-associated protein 1 (HAP-1)	0.87	-	nuc	0		early endosome [TAS] late endosome [TAS]			629
P53159 UniProt NPD GO	YGH5_YEAST	Hypothetical 44.6 kDa protein in RPL7A-HSF1 intergenic region	0.87	-	nuc	0		nuclear envelope [IDA] spindle pole body [IDA]			387
P58151 UniProt NPD GO	YCXC_ASTLO	Hypothetical 51.9 kDa protein in rps4-rps11 intergenic region (ORF426)	0.87	+	nuc	0	Plastid				426
P36119 UniProt NPD GO	YK03_YEAST	Hypothetical 60.8 kDa protein in YPT52-DBP7 intergenic region	0.87	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			530
O00844 UniProt NPD GO	Y80K_PARPR	Hypothetical 80 kDa protein	0.87	-	nuc	1					682
P87176 UniProt NPD GO	YB1B_SCHPO	Hypothetical RING finger protein C3D6.11c in chromosome II	0.87	-	mit	0					269
O94611 UniProt NPD GO	YFO4_SCHPO	Hypothetical protein C1296.04 in chromosome I	0.87	+	nuc	0					248
Q10324 UniProt NPD GO	YD6C_SCHPO	Hypothetical protein C17G8.12 in chromosome I	0.87	-	nuc	0					608
Q10432 UniProt NPD GO	YQ37_SCHPO	Hypothetical protein C188.07 in chromosome III	0.87	-	nuc	0		chromosome, telomeric region [IDA] nucleoplasm [IDA]			735
Q9Y7J8 UniProt NPD GO	YGL1_SCHPO	Hypothetical protein C216.01c in chromosome II	0.87	-	nuc	0					836
O74871 UniProt NPD GO	YCW3_SCHPO	Hypothetical protein C31H12.03c in chromosome III	0.87	-	nuc	0					245
O14302 UniProt NPD GO	YE86_SCHPO	Hypothetical protein C9G1.06c in chromosome I	0.87	-	nuc	0					886
P34409 UniProt NPD GO	YLW6_CAEEL	Hypothetical protein F22B7.6 in chromosome III	0.87	-	nuc	0					518
P34458 UniProt NPD GO	YMD4_CAEEL	Hypothetical protein F54H12.4	0.87	-	nuc	0					343
P34501 UniProt NPD GO	YMS5_CAEEL	Hypothetical protein K03H1.5 precursor	0.87	-	end	2 *					1385
Q09370 UniProt NPD GO	YS41_CAEEL	Hypothetical protein ZK177.1	0.87	-	nuc	0					460
Q9QXV3 UniProt NPD GO	ING1_MOUSE	Inhibitor of growth protein 1	0.87	+	nuc	0	Nucleus (By similarity)				279
P53239 UniProt NPD GO	COX18_YEAST	Inner membrane protein COX18, mitochondrial precursor (Cytochrome c oxidase assembly protein 18)	0.87	-	nuc	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [IDA] mitochondrial inner membrane [IDA]			316
Q9Y581 UniProt NPD GO	INSL6_HUMAN	Insulin-like peptide INSL6 precursor (Insulin-like peptide 6) (Relaxin/insulin-like factor 1) [Conta ...	0.87	+	mit	0	Secreted protein (By similarity)		606414		213
P34609 UniProt NPD GO	JIP_CAEEL	JNK-interacting protein (JIP) (JNK MAP kinase scaffold protein) (Uncoordinated protein 16)	0.87	-	nuc	0	Cytoplasm; perinuclear region. Diffusely localized throughout cell body but intensely localized in r ...	axon [IDA] cytoplasm [IEP]			1157
Q9U297 UniProt NPD GO	JHD3_CAEEL	JmjC domain-containing histone demethylation protein 3 (EC 1.14.11.-) (ceJMJD2)	0.87	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			894
O94953 UniProt NPD GO	JHD3B_HUMAN	JmjC domain-containing histone demethylation protein 3B (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.87	-	nuc	0	Nucleus		609765		1096
Q5XUN4 UniProt NPD GO	JAD1D_PANTR	Jumonji/ARID domain-containing protein 1D (SmcY protein)	0.87	-	nuc	0					1535
Q9BY66 UniProt NPD GO	JAD1D_HUMAN	Jumonji/ARID domain-containing protein 1D (SmcY protein) (Histocompatibility Y antigen) (H-Y)	0.87	-	nuc	0			426000		1539
Q08979 UniProt NPD GO	KEL3_YEAST	Kelch repeat-containing protein 3	0.87	-	nuc	0		cytoplasm [IDA]			651
O97961 UniProt NPD GO	KTN1_VULVU	Kinectin	0.87	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Vesicle ...				1330
P97329 UniProt NPD GO	KI20A_MOUSE	Kinesin family member 20A (Rabkinesin-6) (Rab6-interacting kinesin-like protein) (Kinesin-like prote ...	0.87	-	nuc	0	Golgi apparatus				887
P33173 UniProt NPD GO	KIF1A_MOUSE	Kinesin-like protein KIF1A (Axonal transporter of synaptic vesicles)	0.87	-	nuc	0				1VFZ	1695
Q60575 UniProt NPD GO	KIF1B_MOUSE	Kinesin-like protein KIF1B	0.87	-	nuc	0	Cytoplasmic vesicle. Predominantly found on the vesicle- and tubule-like structures within the cytop ...	cytoplasmic vesicle membrane [IDA] microtubule associated complex [IDA] mitochondrion [IDA]			1816
P28741 UniProt NPD GO	KIF3A_MOUSE	Kinesin-like protein KIF3A (Microtubule plus end-directed kinesin motor 3A)	0.87	+	nuc	0					701

You are viewing entries 5601 to 5650 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.