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
Q875B7 UniProt NPD GO	H2B_PODAN	Histone H2B	0.47	-	nuc	0	Nucleus (By similarity)				136
O75446 UniProt NPD GO	SAP30_HUMAN	Histone deacetylase complex subunit SAP30 (Sin3-associated polypeptide, 30 kDa) (Sin3 corepressor co ...	0.47	-	nuc	0	Nucleus	histone deacetylase complex [TAS]	603378		220
P18111 UniProt NPD GO	CDX1_MOUSE	Homeobox protein CDX-1 (Caudal-type homeobox protein 1)	0.47	+	nuc	0	Nucleus				268
P09078 UniProt NPD GO	HXB8_PIG	Homeobox protein Hox-B8 (Hox-2.4) (Fragment)	0.47	+	mit	0	Nucleus				93
Q9Z214 UniProt NPD GO	HOME1_RAT	Homer protein homolog 1 (PSD-Zip45) (VASP/Ena-related gene up-regulated during seizure and LTP)	0.47	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells. Isoform 1 inhibits surface expres ...			1I2H	366
P12917 UniProt NPD GO	MET2_ASCIM	Homoserine O-acetyltransferase (EC 2.3.1.31) (Homoserine O-trans-acetylase)	0.47	-	nuc	0					518
P47162 UniProt NPD GO	YJ98_YEAST	Hypothetical 13.5 kDa protein in ZMS1-MNS1 intergenic region	0.47	-	nuc	0					119
P43580 UniProt NPD GO	YFB2_YEAST	Hypothetical 17.2 kDa protein in HSP12-HXT10 intergenic region	0.47	-	nuc	0					148
Q04257 UniProt NPD GO	YMA3_YEAST	Hypothetical 34.0 kDa protein in GLO1-YPT7 intergenic region	0.47	-	nuc	0					290
P40508 UniProt NPD GO	YIH7_YEAST	Hypothetical 36.9 kDa protein in THS1-SEC28 intergenic region	0.47	-	nuc	2		mitochondrion [IDA]			320
P38451 UniProt NPD GO	YMF02_MARPO	Hypothetical 37.0 kDa protein in RPS2 3'region (ORF 322)	0.47	-	end	3 *					322
P36152 UniProt NPD GO	YK51_YEAST	Hypothetical 38.5 kDa protein in MET1-SIS2 intergenic region	0.47	-	nuc	0		cytoplasm [IDA]			348
P38779 UniProt NPD GO	YHL2_YEAST	Hypothetical 42.5 kDa protein in COX6-CUP1 intergenic region	0.47	-	nuc	0		nucleolus [IDA] proteasome complex (sensu Eukaryota) [IDA]			376
P38292 UniProt NPD GO	YB18_YEAST	Hypothetical 48.6 kDa protein in TYR1-SSE2 intergenic region	0.47	-	vac	4	Membrane; multi-pass membrane protein (Potential)	integral to peroxisomal membrane [IDA]			413
P47084 UniProt NPD GO	YJX3_YEAST	Hypothetical 62.2 kDa protein in MPP10-SAG1 intergenic region	0.47	-	cyt	0		mitochondrion [IDA]			539
O74347 UniProt NPD GO	YO87_SCHPO	Hypothetical UPF0287 protein C21D10.07 in chromosome II	0.47	+	nuc	0					104
P54245 UniProt NPD GO	YZN4_CAEEL	Hypothetical acetylcholine receptor-like protein F18G5.4 precursor	0.47	-	end	2	Membrane; multi-pass membrane protein				615
Q11122 UniProt NPD GO	YX11_CAEEL	Hypothetical protein C03F11.1	0.47	-	end	5	Membrane; multi-pass membrane protein (Potential)				471
Q9Y824 UniProt NPD GO	YON1_SCHPO	Hypothetical protein C1105.01 in chromosome II	0.47	-	nuc	0					1001
O13715 UniProt NPD GO	YDZ8_SCHPO	Hypothetical protein C14C4.08 in chromosome I	0.47	-	nuc	0					179
O36033 UniProt NPD GO	YLM1_SCHPO	Hypothetical protein C19B12.01 in chromosome I	0.47	-	nuc	0					817
Q09721 UniProt NPD GO	YA4A_SCHPO	Hypothetical protein C31A2.10 in chromosome I	0.47	-	mit	0					460
Q10180 UniProt NPD GO	YAW5_SCHPO	Hypothetical protein C3F10.05c in chromosome I	0.47	-	nuc	0					326
Q8SW78 UniProt NPD GO	Y309_ENCCU	Hypothetical protein ECU03_0090	0.47	+	cyt	0					622
Q8SVP4 UniProt NPD GO	Y4G5_ENCCU	Hypothetical protein ECU04_1650	0.47	-	nuc	0					117
Q8STI4 UniProt NPD GO	YA60_ENCCU	Hypothetical protein ECU10_0060/ECU11_2080i	0.47	-	cyt	0					283
Q19895 UniProt NPD GO	YUQP_CAEEL	Hypothetical protein F28H7.8 in chromosome V	0.47	-	cyt	0					410
Q09319 UniProt NPD GO	YQZ1_CAEEL	Hypothetical protein F40B5.1	0.47	-	nuc	0					174
Q6BEV5 UniProt NPD GO	YRMC_CAEEL	Hypothetical protein R06F6.12	0.47	-	nuc	0					417
P93303 UniProt NPD GO	YMF19_ARATH	Hypothetical protein ymf19 (ORFB)	0.47	-	mit	1 *	Mitochondrion				158
P52170 UniProt NPD GO	IMA1_XENLA	Importin alpha-1 subunit (Karyopherin alpha-1 subunit)	0.47	-	cyt	0	Cytoplasm. Nucleus				521
Q96321 UniProt NPD GO	IMA1_ARATH	Importin alpha-1 subunit (Karyopherin alpha-1 subunit) (KAP alpha)	0.47	-	nuc	0	Cytoplasm (By similarity)				532
Q9SZT9 UniProt NPD GO	GH32_ARATH	Indole-3-acetic acid-amido synthetase GH3.2 (EC 6.3.2.-) (Auxin-responsive GH3-like protein 2) (AtGH ...	0.47	-	cyt	0					549
Q5ZKY4 UniProt NPD GO	ING4_CHICK	Inhibitor of growth protein 4 (p29ING4)	0.47	-	nuc	0	Nucleus (By similarity)				249
Q8BWD2 UniProt NPD GO	IP6K3_MOUSE	Inositol hexaphosphate kinase 3 (EC 2.7.4.21) (InsP6 kinase 3) (Inositol hexakisphosphate kinase 3)	0.47	-	nuc	0	Cytoplasm (By similarity)	nucleus [IDA]			396
P17085 UniProt NPD GO	IGF1_ONCKI	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.47	-	nuc	0	Secreted protein				188
P23695 UniProt NPD GO	IGF2_PIG	Insulin-like growth factor II precursor (IGF-II)	0.47	-	exc	0	Secreted protein				181
P35572 UniProt NPD GO	IBP6_RAT	Insulin-like growth factor-binding protein 6 precursor (IGFBP-6) (IBP-6) (IGF-binding protein 6)	0.47	-	nuc	0	Secreted protein				226
P20701 UniProt NPD GO	ITAL_HUMAN	Integrin alpha-L precursor (Leukocyte adhesion glycoprotein LFA-1 alpha chain) (LFA-1A) (Leukocyte f ...	0.47	-	end	2 *	Membrane; single-pass type I membrane protein	integrin complex [NAS]	153370	1ZOP	1170
P11835 UniProt NPD GO	ITB2_MOUSE	Integrin beta-2 precursor (Cell surface adhesion glycoproteins LFA-1/CR3/P150,95 subunit beta) (Comp ...	0.47	-	end	1	Membrane; single-pass type I membrane protein				771
P97278 UniProt NPD GO	ITIH1_MESAU	Inter-alpha-trypsin inhibitor heavy chain H1 precursor (ITI heavy chain H1) (Inter-alpha-inhibitor h ...	0.47	-	cyt	1 *					914
Q9QXX2 UniProt NPD GO	IFNG_SIGHI	Interferon gamma precursor (IFN-gamma)	0.47	-	exc	0	Secreted protein (By similarity)				170
Q90643 UniProt NPD GO	IRF3_CHICK	Interferon regulatory factor 3 (IRF-3)	0.47	-	nuc	0	Nucleus				491
Q13568 UniProt NPD GO	IRF5_HUMAN	Interferon regulatory factor 5 (IRF-5)	0.47	-	nuc	0	Nucleus		607218		498
O14879 UniProt NPD GO	IFIT3_HUMAN	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT-3) (IFIT-4) (Interferon-induced 60 ...	0.47	-	nuc	0			604650		490
P54349 UniProt NPD GO	IL12A_BOVIN	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.47	-	mit	0	Secreted protein	extracellular space [NAS]			221
Q865Y2 UniProt NPD GO	IL12A_PAPAN	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.47	-	mit	0	Secreted protein (By similarity)				219
P41690 UniProt NPD GO	IL2RA_FELCA	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (CD25 ...	0.47	-	cyt	1	Membrane; single-pass type I membrane protein				275
Q38J85 UniProt NPD GO	IL2RB_MACFA	Interleukin-2 receptor beta chain precursor (IL-2 receptor) (P70-75) (High affinity IL-2 receptor su ...	0.47	-	exc	2 *	Membrane; single-pass type I membrane protein (By similarity)				551
Q9S7H8 UniProt NPD GO	ICS1_ARATH	Isochorismate synthase 1, chloroplast precursor (EC 5.4.4.2) (IcsI) (Isochorismate mutase) (Salicyli ...	0.47	-	mit	0	Plastid; chloroplast (Potential)				569

You are viewing entries 27001 to 27050 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.