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
P59940 UniProt NPD GO	KGX4C_CENSC	Potassium channel toxin gamma-KTx 4.12 (Neurotoxin CsEKerg1)	0.06	-	nuc	0	Secreted protein				43
Q86QV7 UniProt NPD GO	KGX42_CENNO	Potassium channel toxin gamma-KTx 4.2 (Ergtoxin-like protein 5) (ErgTx5) (CnErg5) (CnErgTx5)	0.06	-	nuc	0	Secreted protein				43
Q86QU2 UniProt NPD GO	KGX51_CENSC	Potassium channel toxin gamma-KTx 5.1 (Ergtoxin-like protein 5) (ErgTx5) (CsErg5) (CsErgTx5)	0.06	-	nuc	0	Secreted protein				47
P23299 UniProt NPD GO	KCNE1_MOUSE	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.06	-	mit	1 *	Membrane; single-pass type I membrane protein				129
P18434 UniProt NPD GO	ATP4B_PIG	Potassium-transporting ATPase subunit beta (Proton pump beta chain) (Gastric H(+)/K(+) ATPase beta s ...	0.06	-	cyt	1 *	Membrane; single-pass type II membrane protein				290
P83500 UniProt NPD GO	PA55H_SHEEP	Pregnancy-associated glycoprotein 55h (EC 3.4.23.-) (ovPAG 55h) (Fragment)	0.06	-		0					20
P83493 UniProt NPD GO	PA58A_SHEEP	Pregnancy-associated glycoprotein 58a (EC 3.4.23.-) (ovPAG 58a) (Fragment)	0.06	-		0					20
P83495 UniProt NPD GO	PA58C_SHEEP	Pregnancy-associated glycoprotein 58c (EC 3.4.23.-) (ovPAG 58c) (Fragment)	0.06	-	nuc	0					23
P80934 UniProt NPD GO	PAG59_CAPHI	Pregnancy-associated glycoprotein 59 (EC 3.4.23.-) (PAG 59) (Fragment)	0.06	-	cyt	0					27
P83494 UniProt NPD GO	PA61B_SHEEP	Pregnancy-associated glycoprotein 61b (EC 3.4.23.-) (ovPAG 61b) (Fragment)	0.06	-		0					18
Q8HY39 UniProt NPD GO	PRAF1_CANFA	Prenylated Rab acceptor protein 1 (PRA1 family protein 1)	0.06	-	end	2	Cell membrane; multi-pass membrane protein (By similarity). Cytoplasm (By similarity). Golgi apparat ...				185
O35394 UniProt NPD GO	PRAF1_RAT	Prenylated Rab acceptor protein 1 (PRA1 family protein 1)	0.06	-	end	2	Cell membrane; multi-pass membrane protein. Cytoplasm. Golgi apparatus. Synaptic vesicle. According ...				185
P20049 UniProt NPD GO	TYR1_YEAST	Prephenate dehydrogenase [NADP+] (EC 1.3.1.13) (PRDH)	0.06	-	cyt	0		cytoplasm [IDA]			452
P28527 UniProt NPD GO	SECY_GUITH	Preprotein translocase secY subunit	0.06	-	end	9 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				420
O62688 UniProt NPD GO	MCH_PANPA	Pro-MCH precursor (Fragment)	0.06	-	exc	1 *	Secreted protein (By similarity)				71
O62689 UniProt NPD GO	MCH_PANTR	Pro-MCH precursor (Fragment)	0.06	-	exc	1 *	Secreted protein (By similarity)				71
P91119 UniProt NPD GO	PDE5_CAEEL	Probable 3',5'-cyclic phosphodiesterase pde-5 (EC 3.1.4.17)	0.06	-	nuc	0					393
Q4WPV8 UniProt NPD GO	HPPD2_ASPFU	Probable 4-hydroxyphenylpyruvate dioxygenase 2 (EC 1.13.11.27) (4HPPD 2) (HPD 2) (HPPDase 2)	0.06	-	cyt	0					406
Q9Y7Z2 UniProt NPD GO	ARF2_SCHPO	Probable ADP-ribosylation factor	0.06	-	cyt	0					184
P90921 UniProt NPD GO	ATPL1_CAEEL	Probable ATP synthase subunit g 1, mitochondrial (EC 3.6.3.14)	0.06	-	nuc	0					131
Q9WV35 UniProt NPD GO	ABEC2_MOUSE	Probable C->U-editing enzyme APOBEC-2 (EC 3.5.4.-)	0.06	-	cyt	0					224
Q8GUK6 UniProt NPD GO	PIS2_ARATH	Probable CDP-diacylglycerol--inositol 3-phosphatidyltransferase 2 (EC 2.7.8.11) (Phosphatidylinosito ...	0.06	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				225
P46090 UniProt NPD GO	GPR1_RAT	Probable G-protein coupled receptor 1	0.06	-	end	7 *	Membrane; multi-pass membrane protein				353
Q8TDV2 UniProt NPD GO	GP148_HUMAN	Probable G-protein coupled receptor 148 (G-protein coupled receptor PGR6) (Brain and testis restrict ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				347
Q3ZBK9 UniProt NPD GO	GP171_BOVIN	Probable G-protein coupled receptor 171	0.06	-	end	6 *	Membrane; multi-pass membrane protein				319
Q99679 UniProt NPD GO	GPR21_HUMAN	Probable G-protein coupled receptor 21	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601909		349
Q49SP8 UniProt NPD GO	GPR33_RATRT	Probable G-protein coupled receptor 33	0.06	-	end	7 *	Membrane; multi-pass membrane protein				339
Q9BZJ8 UniProt NPD GO	GPR61_HUMAN	Probable G-protein coupled receptor 61 (Biogenic amine receptor-like G-protein coupled receptor)	0.06	-	end	7 *	Membrane; multi-pass membrane protein		606916		451
Q9V817 UniProt NPD GO	MTH4_DROME	Probable G-protein coupled receptor Mth-like 4 precursor (Protein methuselah-like 4)	0.06	-	end	7	Membrane; multi-pass membrane protein (Potential)				480
Q9FLX7 UniProt NPD GO	NDUA5_ARATH	Probable NADH-ubiquinone oxidoreductase 18 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6 ...	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				169
Q09870 UniProt NPD GO	RCL1_SCHPO	Probable RNA 3'-terminal phosphate cyclase-like protein	0.06	-	mit	0	Nucleus; nucleolus (By similarity)				363
Q18493 UniProt NPD GO	UAP1_CAEEL	Probable UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)	0.06	-	cyt	0	Cytoplasm (By similarity)				484
Q8H0B2 UniProt NPD GO	ARAE3_ORYSA	Probable UDP-arabinose 4-epimerase 3 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 3) (UDP-galactose 4-epim ...	0.06	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Potential) ...				406
P78773 UniProt NPD GO	ACSA_SCHPO	Probable acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.06	-	nuc	0					662
Q9C0V0 UniProt NPD GO	YQD2_SCHPO	Probable amino-acid permease PB1C11.02	0.06	-	end	11 *	Membrane; multi-pass membrane protein				505
Q22067 UniProt NPD GO	AATC_CAEEL	Probable aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloaceta ...	0.06	-	cyt	0	Cytoplasm (Potential)				408
Q5VP70 UniProt NPD GO	PIN3A_ORYSA	Probable auxin efflux carrier component 3a (OsPIN3a)	0.06	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				618
Q4WQV2 UniProt NPD GO	CUTI2_ASPFU	Probable cutinase 2 precursor (EC 3.1.1.74) (Cutin hydrolase 2)	0.06	-	end	0	Secreted protein (By similarity)				214
Q2TZY7 UniProt NPD GO	CUTI2_ASPOR	Probable cutinase 2 precursor (EC 3.1.1.74) (Cutin hydrolase 2)	0.06	-	exc	0	Secreted protein (By similarity)				221
O23138 UniProt NPD GO	CYC2_ARATH	Probable cytochrome c At1g22840	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix				114
P30648 UniProt NPD GO	DCTD_CAEEL	Probable deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.06	-	cyt	0					197
Q9CWQ0 UniProt NPD GO	DPH5_MOUSE	Probable diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.06	-	cyt	0					281
Q96VG2 UniProt NPD GO	OST4_SCHPO	Probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase 4 kDa subunit (EC 2.4.1.119) ...	0.06	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				32
Q11174 UniProt NPD GO	CHIT_CAEEL	Probable endochitinase (EC 3.2.1.14)	0.06	-	mit	0					617
P34559 UniProt NPD GO	ECHM_CAEEL	Probable enoyl-CoA hydratase, mitochondrial (EC 4.2.1.17)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				288
O14230 UniProt NPD GO	FPPS_SCHPO	Probable farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) ...	0.06	-	cyt	0	Cytoplasm (By similarity)				347
P14325 UniProt NPD GO	SYQ_DICDI	Probable glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS) (Vegetative-speci ...	0.06	-	nuc	0					287
Q9S9K7 UniProt NPD GO	H2AXB_ARATH	Probable histone H2AXb (HTA3)	0.06	-	nuc	0	Nucleus (By similarity)				142
Q93353 UniProt NPD GO	IDH3B_CAEEL	Probable isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41) (Isocitr ...	0.06	-	mit	0	Mitochondrion (By similarity)				379
P07191 UniProt NPD GO	MAL1_DROME	Probable maltase D precursor (EC 3.2.1.20) (Larval visceral protein D)	0.06	-	exc	0					567

You are viewing entries 72851 to 72900 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.