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
Q8WNY1 UniProt NPD GO	GREM1_MACMU	Gremlin-1 precursor	0.77	-	exc	0	Secreted protein (Probable)				184
O60565 UniProt NPD GO	GREM1_HUMAN	Gremlin-1 precursor (Cysteine knot superfamily 1, BMP antagonist 1) (Proliferation-inducing gene 2 p ...	0.77	-	exc	0	Secreted protein (Probable)	extracellular space [TAS]	603054		184
Q14449 UniProt NPD GO	GRB14_HUMAN	Growth factor receptor-bound protein 14 (GRB14 adapter protein)	0.77	+	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Endosome; endosomal membran ...		601524	2AUH	540
Q66NC0 UniProt NPD GO	GDF9_CAPHI	Growth/differentiation factor 9 precursor (GDF-9)	0.77	-	exc	0	Secreted protein (By similarity)				453
P39717 UniProt NPD GO	GPB2_YEAST	Guanine nucleotide-binding protein subunit beta 2 (Gbeta mimic Kelch protein 2)	0.77	-	nuc	0	Cytoplasm. Mitochondrion	cytoplasm [IDA] mitochondrion [IDA] plasma membrane [IDA]			880
Q8MT06 UniProt NPD GO	GNL3_DROME	Guanine nucleotide-binding protein-like 3 homolog (Nucleostemin homolog)	0.77	+	nuc	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			581
P54198 UniProt NPD GO	HIRA_HUMAN	HIRA protein (TUP1-like enhancer of split protein 1)	0.77	+	nuc	0	Nucleus. Primarily, though not exclusively, localized to the nucleus	nucleus [TAS]	600237		1017
O60381 UniProt NPD GO	HBP1_HUMAN	HMG box-containing protein 1 (HMG box transcription factor 1) (High mobility group box transcription ...	0.77	-	nuc	0	Nucleus				514
Q9QUS4 UniProt NPD GO	HEY2_MOUSE	Hairy/enhancer-of-split related with YRPW motif 2 (Hairy and enhancer of split-related protein 2) (H ...	0.77	-	nuc	0	Nucleus (Probable)				339
Q9Z136 UniProt NPD GO	TSC1_RAT	Hamartin (Tuberous sclerosis 1 protein homolog)	0.77	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). At steady state fo ...	growth cone [IDA]			1163
P38531 UniProt NPD GO	HSF3_CHICK	Heat shock factor protein 3 (HSF 3) (Heat shock transcription factor 3) (HSTF 3) (HSF 3C) (HSTF 3C)	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic during normal growth and moves to th ...				467
Q03365 UniProt NPD GO	HNF1B_PIG	Hepatocyte nuclear factor 1-beta (HNF-1beta) (HNF-1B) (Variant hepatic nuclear factor 1) (VHNF1) (FP ...	0.77	+	nuc	0	Nucleus				559
P40644 UniProt NPD GO	HMGH_STRPU	High mobility group protein 1 homolog	0.77	+	nuc	0	Nucleus				200
P0C1H6 UniProt NPD GO	H2BFM_HUMAN	Histone H2B type F-M (H2B.s) (H2B/s)	0.77	-	nuc	0	Nucleus				257
P83038 UniProt NPD GO	HDAC4_CHICK	Histone deacetylase 4 (HD4)	0.77	-	nuc	0	Nucleus (By similarity)	histone deacetylase complex [TAS]			1080
Q9FF80 UniProt NPD GO	SUVH1_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH1 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.77	-	nuc	0	Nucleus. Associates with centromeric constitutive heterochromatin				670
Q04743 UniProt NPD GO	EMX2_HUMAN	Homeobox protein EMX2 (Empty spiracles homolog 2) (Empty spiracles-like protein 2)	0.77	+	nuc	0	Nucleus (Probable)	nucleus [NAS]	600035		252
Q04744 UniProt NPD GO	EMX2_MOUSE	Homeobox protein EMX2 (Empty spiracles homolog 2) (Empty spiracles-like protein 2)	0.77	+	nuc	0	Nucleus (Probable)				253
Q8SVT6 UniProt NPD GO	HD6_ENCCU	Homeobox protein HD-6 (EcHD-6)	0.77	-	nuc	0	Nucleus				121
Q6W990 UniProt NPD GO	HXADA_BRARE	Homeobox protein Hox-A13a	0.77	+	nuc	0	Nucleus (By similarity)				310
Q9IA23 UniProt NPD GO	HXA5_HETFR	Homeobox protein Hox-A5	0.77	+	nuc	0	Nucleus (By similarity)				275
P51783 UniProt NPD GO	HXA9_CAVPO	Homeobox protein Hox-A9 (Hox-1.7) (Fragment)	0.77	+	nuc	0	Nucleus				162
P09014 UniProt NPD GO	HXB5A_BRARE	Homeobox protein Hox-B5a (Hox-B5) (Zf-21)	0.77	+	nuc	0	Nucleus				275
P09013 UniProt NPD GO	HXB5B_BRARE	Homeobox protein Hox-B5b (Hox-B5-like) (Zf-54)	0.77	+	nuc	0	Nucleus				276
P20615 UniProt NPD GO	HXB9_MOUSE	Homeobox protein Hox-B9 (Hox-2.5)	0.77	+	nuc	0	Nucleus				250
Q9PWM2 UniProt NPD GO	HXB9A_BRARE	Homeobox protein Hox-B9a (Hox-B9)	0.77	+	nuc	0	Nucleus (By similarity)				249
Q9NYD6 UniProt NPD GO	HXC10_HUMAN	Homeobox protein Hox-C10	0.77	+	nuc	0	Nucleus		605560		342
P32442 UniProt NPD GO	MEOX1_MOUSE	Homeobox protein MOX-1 (Mesenchyme homeobox 1)	0.77	+	nuc	0	Nucleus (Potential)				253
O42406 UniProt NPD GO	SIX3_CHICK	Homeobox protein SIX3 (Sine oculis homeobox homolog 3) (CSIX3)	0.77	-	nuc	0	Nucleus (By similarity)				314
P09065 UniProt NPD GO	HME1_MOUSE	Homeobox protein engrailed-1 (Mo-En-1)	0.77	+	nuc	0	Nucleus				401
P09066 UniProt NPD GO	HME2_MOUSE	Homeobox protein engrailed-2 (Mo-En-2)	0.77	+	nuc	0	Nucleus				324
O75360 UniProt NPD GO	PROP1_HUMAN	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.77	+	nuc	0	Nucleus (By similarity)		601538		226
Q3LU41 UniProt NPD GO	PROP1_THEGE	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.77	+	nuc	0	Nucleus (By similarity)				226
Q9ERH7 UniProt NPD GO	HIPK3_MOUSE	Homeodomain-interacting protein kinase 3 (EC 2.7.11.1) (Fas-interacting serine/threonine-protein kin ...	0.77	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [ISS]			1192
P09077 UniProt NPD GO	SCR_DROME	Homeotic protein Sex combs reduced	0.77	+	nuc	0	Nucleus				417
P40156 UniProt NPD GO	YNV3_YEAST	Hypothetical 25.3 kDa protein in PEX17-MER1 intergenic region	0.77	-	nuc	0					214
P53882 UniProt NPD GO	YNR6_YEAST	Hypothetical 67.4 kDa protein in RPS3-PSD1 intergenic region	0.77	-	nuc	1		vacuole (sensu Fungi) [IDA]			636
P36056 UniProt NPD GO	YKP5_YEAST	Hypothetical 72.2 kDa protein in RPS27A-GPM1 intergenic region	0.77	-	mit	0		mitochondrial small ribosomal subunit [IDA]			628
P68349 UniProt NPD GO	DOF12_ARATH	Hypothetical Dof zinc finger protein DOF1.2 (AtDOF1.2)	0.77	+	nuc	0	Nucleus (Probable)				260
Q18262 UniProt NPD GO	YPI7_CAEEL	Hypothetical F-box protein C27F2.7	0.77	-	nuc	0					408
Q10948 UniProt NPD GO	YMP4_CAEEL	Hypothetical protein B0361.4	0.77	-	nuc	2					374
Q09742 UniProt NPD GO	YB61_SCHPO	Hypothetical protein C12C2.01c in chromosome II	0.77	-	mit	0					318
Q09867 UniProt NPD GO	YAG2_SCHPO	Hypothetical protein C12G12.02 in chromosome I	0.77	-	nuc	0					183
Q18232 UniProt NPD GO	YBRI_CAEEL	Hypothetical protein C26F1.3	0.77	+	nuc	0					186
Q09911 UniProt NPD GO	YAJE_SCHPO	Hypothetical protein C30D11.14c in chromosome I	0.77	-	nuc	0					534
Q09829 UniProt NPD GO	YAD3_SCHPO	Hypothetical protein C4G8.03c in chromosome I	0.77	-	nuc	0					780
O74939 UniProt NPD GO	YJB1_SCHPO	Hypothetical protein C553.01c in chromosome III	0.77	-	nuc	0					715
P34560 UniProt NPD GO	YNP7_CAEEL	Hypothetical protein T05G5.7	0.77	-	mit	0					293
Q10006 UniProt NPD GO	YRY2_CAEEL	Hypothetical protein T15H9.2	0.77	-	nuc	0					252
Q9U2T3 UniProt NPD GO	Y8CB_CAEEL	Hypothetical protein Y116A8C.11	0.77	-	nuc	0					281

You are viewing entries 10351 to 10400 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.