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
Q9I7I0 UniProt NPD GO	CCNB3_DROME	G2/mitotic-specific cyclin-B3	0.67	-	nuc	0	Nucleus	nucleus [IDA]			575
Q12317 UniProt NPD GO	MSB4_YEAST	GTPase-activating protein MSB4 (Multicopy suppressor of bud emergence 4)	0.67	-	cyt	0	Cytoplasm. Bud. Bud neck. Localizes to the presumptive bud site, the bud tip and the mother-bud neck ...	bud tip [IDA] incipient bud site [IDA]			492
P08431 UniProt NPD GO	GAL7_YEAST	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.67	-	nuc	0		cytoplasm [IDA]			365
P01272 UniProt NPD GO	GLUC_BOVIN	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.67	-	exc	0	Secreted protein			1KX6	180
Q01097 UniProt NPD GO	NMDE2_MOUSE	Glutamate [NMDA] receptor subunit epsilon 2 precursor (N-methyl D-aspartate receptor subtype 2B) (NR ...	0.67	-	end	4	Membrane; multi-pass membrane protein	membrane fraction [IDA] postsynaptic membrane [IDA] presynaptic membrane [IEP] synaptic vesicle [IDA]			1482
Q00960 UniProt NPD GO	NMDE2_RAT	Glutamate [NMDA] receptor subunit epsilon 2 precursor (N-methyl D-aspartate receptor subtype 2B) (NR ...	0.67	-	end	4	Membrane; multi-pass membrane protein	N-methyl-D-aspartate selective glutamate re... [IDA] neuron projection [IDA] presynaptic membrane [IEP] synapse [IEP]			1482
Q61627 UniProt NPD GO	GRID1_MOUSE	Glutamate receptor delta-1 subunit precursor (GluR delta-1)	0.67	-	end	4	Membrane; multi-pass membrane protein (By similarity)				1009
Q62640 UniProt NPD GO	GRID1_RAT	Glutamate receptor delta-1 subunit precursor (GluR delta-1)	0.67	-	end	3	Membrane; multi-pass membrane protein (By similarity)				1009
Q63273 UniProt NPD GO	GRIK5_RAT	Glutamate receptor, ionotropic kainate 5 precursor (Glutamate receptor KA-2) (KA2)	0.67	-	end	3	Membrane; multi-pass membrane protein				979
Q16478 UniProt NPD GO	GRIK5_HUMAN	Glutamate receptor, ionotropic kainate 5 precursor (Glutamate receptor KA-2) (KA2) (Excitatory amino ...	0.67	-	end	3	Membrane; multi-pass membrane protein	integral to membrane [NAS]	600283		980
Q61626 UniProt NPD GO	GRIK5_MOUSE	Glutamate receptor, ionotropic kainate 5 precursor (Glutamate receptor KA-2) (KA2) (Glutamate recept ...	0.67	-	end	3	Membrane; multi-pass membrane protein	ionotropic glutamate receptor complex [IC]			979
P04347 UniProt NPD GO	GLYG5_SOYBN	Glycinin precursor [Contains: Glycinin A3 subunit; Glycinin B4 subunit]	0.67	-	exc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies			1OD5	516
Q9CW79 UniProt NPD GO	GOGA1_MOUSE	Golgin subfamily A member 1 (Golgin-97)	0.67	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein	Golgi apparatus [IDA]			758
Q02108 UniProt NPD GO	GCYA3_HUMAN	Guanylate cyclase soluble subunit alpha-3 (EC 4.6.1.2) (GCS-alpha-3) (Soluble guanylate cyclase larg ...	0.67	-	cyt	0	Cytoplasm	guanylate cyclase complex, soluble [TAS]	139396		690
Q7Z4Q2 UniProt NPD GO	HEAT3_HUMAN	HEAT repeat-containing protein 3	0.67	-	mit	0					680
P63136 UniProt NPD GO	POK17_HUMAN	HERV-K_11q22.1 provirus ancestral Pol protein [Includes: Reverse transcriptase (RT) (EC 2.7.7.49); R ...	0.67	-	nuc	0					954
P63135 UniProt NPD GO	POK12_HUMAN	HERV-K_1q22 provirus ancestral Pol protein (HERV-K102 Pol protein) (HERV-K(III) Pol protein) [Includ ...	0.67	-	end	3					1459
P63145 UniProt NPD GO	GAK11_HUMAN	HERV-K_22q11.21 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K101 Gag protein) [Contai ...	0.67	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
P63126 UniProt NPD GO	GAK4_HUMAN	HERV-K_6q14.1 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K109 Gag protein) (HERV-K(C ...	0.67	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
Q9ULV5 UniProt NPD GO	HSF4_HUMAN	Heat shock factor protein 4 (HSF 4) (Heat shock transcription factor 4) (HSTF 4) (hHSF4)	0.67	-	nuc	0	Nucleus		602438		493
Q4UDU8 UniProt NPD GO	HSP90_THEAN	Heat shock protein 90 (HSP90)	0.67	+	cyt	0					722
Q90474 UniProt NPD GO	HS90A_BRARE	Heat shock protein HSP 90-alpha	0.67	-	cyt	0	Cytoplasm				725
Q96LI6 UniProt NPD GO	HSFY1_HUMAN	Heat shock transcription factor, Y-linked (Heat shock transcription factor 2-like protein) (HSF2-lik ...	0.67	-	nuc	0	Nucleus (Potential)		400029		401
Q9WUU6 UniProt NPD GO	HNF4G_MOUSE	Hepatocyte nuclear factor 4-gamma (HNF-4-gamma)	0.67	-	nuc	0	Nucleus (By similarity)				408
P59438 UniProt NPD GO	HPS5_MOUSE	Hermansky-Pudlak syndrome 5 protein homolog (Ruby-eye protein 2) (Ru2)	0.67	-	nuc	0					1126
Q7XJS0 UniProt NPD GO	ASHR1_ARATH	Histone-lysine N-methyltransferase ASHR1 (EC 2.1.1.43) (ASH1-related protein 1) (Protein SET DOMAIN ...	0.67	-	nuc	0	Nucleus (By similarity)				480
P53774 UniProt NPD GO	DLL2_XENLA	Homeobox protein DLL-2 (XDLL-2)	0.67	+	nuc	0	Nucleus (Potential)				277
P10179 UniProt NPD GO	HMB4_TRIGR	Homeobox protein HB4 (Fragment)	0.67	+	exc	0	Nucleus (Probable)				107
P52949 UniProt NPD GO	HXA5_RAT	Homeobox protein Hox-A5 (Hox-1.3) (Fragment)	0.67	+	nuc	0	Nucleus				233
P20719 UniProt NPD GO	HXA5_HUMAN	Homeobox protein Hox-A5 (Hox-1C)	0.67	+	nuc	0	Nucleus	nucleus [NAS]	142952		270
P02830 UniProt NPD GO	HXA7_MOUSE	Homeobox protein Hox-A7 (Hox-1.1) (M6-12) (M6)	0.67	+	nuc	0	Nucleus				229
Q90423 UniProt NPD GO	HXB1B_BRARE	Homeobox protein Hox-B1b (Hox-A1)	0.67	+	nuc	0	Nucleus				307
P14839 UniProt NPD GO	HXB6_CHICK	Homeobox protein Hox-B6 (GHOX-2.2) (Fragment)	0.67	+	nuc	0	Nucleus				84
Q9TT89 UniProt NPD GO	HXB7_BOVIN	Homeobox protein Hox-B7	0.67	+	nuc	0	Nucleus				217
O70477 UniProt NPD GO	PKNX1_MOUSE	Homeobox protein PKNOX1 (PBX/knotted homeobox 1)	0.67	-	nuc	0	Nucleus (Probable)	transcription factor complex [IDA]			435
Q05502 UniProt NPD GO	HHEX_CHICK	Homeobox protein PRH (Hematopoietically expressed homeobox)	0.67	+	nuc	0	Nucleus (Probable)				277
P54269 UniProt NPD GO	CAUP_DROME	Homeobox protein caupolican	0.67	-	nuc	0	Nucleus (Probable)				693
Q02591 UniProt NPD GO	GSC_MOUSE	Homeobox protein goosecoid	0.67	+	nuc	0	Nucleus				256
P56668 UniProt NPD GO	KNX11_MAIZE	Homeobox protein knotted-1-like 11 (Fragment)	0.67	+	nuc	0	Nucleus (Probable)				88
P10105 UniProt NPD GO	LAB_DROME	Homeotic protein labial (F24) (F90-2)	0.67	+	nuc	0	Nucleus				635
Q05469 UniProt NPD GO	LIPS_HUMAN	Hormone-sensitive lipase (EC 3.1.1.79) (HSL)	0.67	-	nuc	0			151750		1076
O75146 UniProt NPD GO	HIP1R_HUMAN	Huntingtin-interacting protein 1-related protein (Hip1-related) (Hip 12)	0.67	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Intracytoplasmic membrane (By similarity). Membrane-a ...	clathrin-coated vesicle [NAS] coated pit [NAS]	605613	1R0D	1068
P53908 UniProt NPD GO	YNO3_YEAST	Hypothetical 15.3 kDa protein in MFA2-MEP2 intergenic region	0.67	+	nuc	2					130
P40161 UniProt NPD GO	YNU6_YEAST	Hypothetical 51.6 kDa protein in SSB2-SPX18 intergenic region	0.67	-	nuc	0		nucleus [IDA]			455
P53983 UniProt NPD GO	YNA8_YEAST	Hypothetical 76.7 kDa protein in SPO1-SIS1 intergenic region	0.67	+	end	4	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum membrane [IGI]			669
Q95QN6 UniProt NPD GO	YQOE_CAEEL	Hypothetical RING finger protein EEED8.16 in chromosome II	0.67	-	nuc	0					590
Q11101 UniProt NPD GO	YL15_CAEEL	Hypothetical homeobox protein C02F12.5 in chromosome X	0.67	+	nuc	0	Nucleus (Probable)				252
Q11186 UniProt NPD GO	YPD7_CAEEL	Hypothetical protein C05D11.7	0.67	-	end	2 *					621
Q10274 UniProt NPD GO	YD3A_SCHPO	Hypothetical protein C13G7.10 in chromosome I	0.67	-	nuc	0					390
O94306 UniProt NPD GO	YCGJ_SCHPO	Hypothetical protein C16C4.19 in chromosome III	0.67	+	nuc	0					184

You are viewing entries 15251 to 15300 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.