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
Q9Y6N9 UniProt NPD GO	USH1C_HUMAN	Harmonin (Usher syndrome type-1C protein) (Autoimmune enteropathy-related antigen AIE-75) (Antigen N ...	0.39	-	cyt	0			276900	1X5N	552
Q9CZJ2 UniProt NPD GO	HS12B_MOUSE	Heat shock 70 kDa protein 12B	0.39	+	cyt	0					685
P11146 UniProt NPD GO	HSP7B_DROME	Heat shock 70 kDa protein cognate 2 (Heat shock 70 kDa protein 87D)	0.39	-	cyt	0					633
Q96320 UniProt NPD GO	HSF4_ARATH	Heat shock factor protein 4 (HSF 4) (Heat shock transcription factor 4) (HSTF 4)	0.39	-	cyt	0	Nucleus (By similarity)				284
Q10284 UniProt NPD GO	HSP75_SCHPO	Heat shock protein sks2 (Heat shock cognate protein hsc1)	0.39	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide (By s ...				613
Q28270 UniProt NPD GO	CD34_CANFA	Hematopoietic progenitor cell antigen CD34 precursor	0.39	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [ISS]			389
Q9Y661 UniProt NPD GO	OST4_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 4 (EC 2.8.2.23) (Heparan sulfate D-glucosaminyl 3-O ...	0.39	-	nuc	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	extracellular region [NAS]	604059		456
P51968 UniProt NPD GO	RO31_XENLA	Heterogeneous nuclear ribonucleoprotein A3 homolog 1 (hnRNP A3(A))	0.39	+	cyt	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				373
Q14103 UniProt NPD GO	HNRPD_HUMAN	Heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) (AU-rich element RNA-binding protein 1)	0.39	-	nuc	0	Nucleus. Component of ribonucleosomes	nucleus [NAS]	601324	1X0F	355
Q60668 UniProt NPD GO	HNRPD_MOUSE	Heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) (AU-rich element RNA-binding protein 1)	0.39	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				355
Q9JJ54 UniProt NPD GO	HNRPD_RAT	Heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) (AU-rich element RNA-binding protein 1)	0.39	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)	cytosol [IDA]			353
Q5RA82 UniProt NPD GO	HNRPC_PONPY	Heterogeneous nuclear ribonucleoproteins C (hnRNP C)	0.39	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				306
P07910 UniProt NPD GO	HNRPC_HUMAN	Heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNP C1 / hnRNP C2)	0.39	-	nuc	0	Nucleus. Component of ribonucleosomes	spliceosome complex [IDA]	164020	1WF2	306
Q9UV10 UniProt NPD GO	HET6_NEUCR	Heterokaryon incompatibility protein 6, OR allele (Het-6(OR))	0.39	-	cyt	0					680
O49354 UniProt NPD GO	COQ3_ARATH	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.39	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)				322
P53551 UniProt NPD GO	H1_YEAST	Histone H1	0.39	-	nuc	0	Nucleus (Potential)	nuclear nucleosome [IPI] nucleus [IDA]		1YQA	258
Q8SRE2 UniProt NPD GO	H2B_ENCCU	Histone H2B	0.39	-	nuc	0	Nucleus (By similarity)				130
Q6C4I7 UniProt NPD GO	H2B_YARLI	Histone H2B	0.39	-	nuc	0	Nucleus (By similarity)				138
Q8J1L3 UniProt NPD GO	H4_ARXAD	Histone H4	0.39	-	cyt	0	Nucleus (By similarity)				102
Q8LPU4 UniProt NPD GO	HAT1_MAIZE	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48) (Histone acetyltransferase HAT B) ( ...	0.39	+	cyt	0	Nucleus. Cytoplasm				468
P87314 UniProt NPD GO	HIRL_SCHPO	Histone transcription regulator 1 homolog	0.39	-	nuc	0	Nucleus	chromatin [IC] nucleus [IDA]			932
Q2VL85 UniProt NPD GO	MSX1_CALGO	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.39	+	nuc	0	Nucleus (By similarity)				297
Q2VL84 UniProt NPD GO	MSX1_CALJA	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.39	+	nuc	0	Nucleus (By similarity)				297
Q2VL87 UniProt NPD GO	MSX1_MACMU	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.39	+	nuc	0	Nucleus (By similarity)				297
Q2VL88 UniProt NPD GO	MSX1_PANTR	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.39	+	nuc	0	Nucleus (By similarity)				297
Q2VL82 UniProt NPD GO	MSX1_SAGOE	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.39	+	nuc	0	Nucleus (By similarity)				297
P28360 UniProt NPD GO	MSX1_HUMAN	Homeobox protein MSX-1 (Msh homeobox 1-like protein) (Hox-7)	0.39	+	nuc	0	Nucleus		608874		297
Q4R588 UniProt NPD GO	HPBP1_MACFA	Hsp70-binding protein 1 (HspBP1) (Heat shock protein-binding protein 1) (Hsp70-interacting protein 1 ...	0.39	-	nuc	0					364
Q5E9Z2 UniProt NPD GO	HABP2_BOVIN	Hyaluronan-binding protein 2 precursor (EC 3.4.21.-) [Contains: Hyaluronan-binding protein 2 50 kDa ...	0.39	-	mit	0	Secreted protein (By similarity). Secreted as an inactive single-chain precursor and is then activat ...				558
Q5DUX7 UniProt NPD GO	RL2H_NYCOV	Hydrogenosomal 60S ribosomal protein L2	0.39	-	mit	0	Hydrogenosome				290
Q2KIE6 UniProt NPD GO	HMCS2_BOVIN	Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor (EC 2.3.3.10) (HMG-CoA synthase) (3-hydr ...	0.39	-	mit	0	Mitochondrion (By similarity)				508
P46593 UniProt NPD GO	HWP1_CANAL	Hyphal wall protein 1 (Cell elongation protein 2)	0.39	-	nuc	0	Hyphal surface				634
P40365 UniProt NPD GO	YJG7_YEAST	Hypothetical 12.7 kDa protein in SMC3-MRPL8 intergenic region	0.39	+	mit	0	Membrane; multi-pass membrane protein (Potential)				116
Q03207 UniProt NPD GO	YMM2_YEAST	Hypothetical 14.5 kDa protein in PHO84-GTR1 intergenic region	0.39	-	nuc	0					126
P38763 UniProt NPD GO	YHI2_YEAST	Hypothetical 29.0 kDa protein in DED81-MYO1 intergenic region	0.39	-	mit	0					256
O78459 UniProt NPD GO	YCX5_GUITH	Hypothetical 7.8 kDa protein (ORF62)	0.39	+	cyt	0	Plastid; chloroplast				62
Q9SX97 UniProt NPD GO	DOF16_ARATH	Hypothetical Dof zinc finger protein DOF1.6 (AtDOF1.6)	0.39	-	nuc	0	Nucleus (Probable)				209
Q09993 UniProt NPD GO	U139_CAEEL	Hypothetical UPF0139 protein K10B2.4 in chromosome II	0.39	-	nuc	0					113
P41849 UniProt NPD GO	YO99_CAEEL	Hypothetical glycine receptor-like protein T20B12.9 in chromosome III	0.39	-	end	4	Membrane; multi-pass membrane protein (Probable)				476
P92529 UniProt NPD GO	M920_ARATH	Hypothetical mitochondrial protein AtMg00920 (ORF215b)	0.39	-	nuc	0	Mitochondrion (Potential)				215
P03881 UniProt NPD GO	YMRF1_YEAST	Hypothetical mitochondrial protein RF1	0.39	-	nuc	0		mitochondrion [TAS]			472
Q7JPQ6 UniProt NPD GO	YMP3_CAEEL	Hypothetical protein B0361.3	0.39	-	nuc	0					627
O42908 UniProt NPD GO	YBAH_SCHPO	Hypothetical protein C119.17 in chromosome II	0.39	-	cyt	0					882
Q09789 UniProt NPD GO	YA9D_SCHPO	Hypothetical protein C13G6.13 in chromosome I	0.39	-	nuc	0					115
Q09465 UniProt NPD GO	YQ59_CAEEL	Hypothetical protein C16C10.9	0.39	-	cyt	0					274
O13770 UniProt NPD GO	YE98_SCHPO	Hypothetical protein C17A5.08 precursor	0.39	-	exc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				210
Q10485 UniProt NPD GO	YDFE_SCHPO	Hypothetical protein C17C9.14 in chromosome I	0.39	-	nuc	0					232
Q10150 UniProt NPD GO	YAT3_SCHPO	Hypothetical protein C1D4.03c in chromosome I	0.39	-	nuc	0					513
Q09929 UniProt NPD GO	YAL7_SCHPO	Hypothetical protein C21E11.07 in chromosome I	0.39	-	mit	0					325
Q10168 UniProt NPD GO	YAUF_SCHPO	Hypothetical protein C26A3.15c in chromosome I	0.39	-	nuc	0		nuclear pore [IDA]			598

You are viewing entries 32651 to 32700 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.