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
Q07010 UniProt NPD GO	HPRT_TRYBB	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.05	-	cyt	0	Cytoplasm				210
P20035 UniProt NPD GO	HGXR_PLAFG	Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) (HGXPRT) (HGXPRTase) (HGPRT)	0.05	-	cyt	0	Cytoplasm			1CJB	231
P07833 UniProt NPD GO	HGXR_PLAFK	Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) (HGXPRT) (HGXPRTase) (HGPRT)	0.05	-	cyt	0	Cytoplasm				231
Q26997 UniProt NPD GO	HGXR_TOXGO	Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) (HGXPRT) (HGXPRTase) (HGPRT)	0.05	-	cyt	0	Cytoplasm			1QK5	230
P51900 UniProt NPD GO	HGXR_TRIFO	Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) (HGXPRT) (HGXPRTase) (HGPRT)	0.05	-	nuc	0	Cytoplasm			1HGX	183
Q9Y5L2 UniProt NPD GO	HIG2_HUMAN	Hypoxia-inducible gene 2 protein	0.05	-	nuc	1 *					63
Q7Z0A3 UniProt NPD GO	CXI13_CONRA	I-superfamily conotoxin R11.13 precursor (Fragment)	0.05	-	nuc	0	Secreted protein				45
Q7Z099 UniProt NPD GO	CXI2_CONRA	I-superfamily conotoxin R11.2 precursor (Fragment)	0.05	-	nuc	0	Secreted protein				46
Q7Z098 UniProt NPD GO	CXI5_CONRA	I-superfamily conotoxin R11.5 precursor (Fragment)	0.05	-	nuc	0	Secreted protein				46
P69498 UniProt NPD GO	CXI_CONMI	I-superfamily conotoxin precursor	0.05	-	exc	1 *	Secreted protein (By similarity)				67
P69501 UniProt NPD GO	CXI2_CONVX	I-superfamily conotoxin-2 precursor	0.05	-	exc	1 *	Secreted protein (By similarity)				67
P54970 UniProt NPD GO	ILL2_ARATH	IAA-amino acid hydrolase ILR1-like 2 precursor (EC 3.5.1.-)	0.05	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)			1XMB	439
P04367 UniProt NPD GO	ANP3_MYOSC	Ice-structuring protein SS-3 (ISP SS-3) (Antifreeze peptide SS-3)	0.05	-	nuc	0				1Y04	33
P01749 UniProt NPD GO	HV05_MOUSE	Ig heavy chain V region 3 precursor	0.05	-	exc	0				1A14	117
P01751 UniProt NPD GO	HV07_MOUSE	Ig heavy chain V region B1-8/186-2 precursor	0.05	-	vac	0				1NQB	139
P01813 UniProt NPD GO	HV01_CAICR	Ig heavy chain V region C3 precursor	0.05	-	exc	0					117
P01745 UniProt NPD GO	HV01_MOUSE	Ig heavy chain V region MPC 11	0.05	-	cyt	0					121
P20956 UniProt NPD GO	HV01_XENLA	Ig heavy chain V region XIG8 precursor (Fragment)	0.05	-	vac	0					136
P01818 UniProt NPD GO	HV2E_HUMAN	Ig heavy chain V-II region HE	0.05	-	mit	0		extracellular region [NAS]			121
P01694 UniProt NPD GO	KV13_RABIT	Ig kappa chain V region 3547	0.05	-	mit	0					110
P01696 UniProt NPD GO	KV15_RABIT	Ig kappa chain V region K29-213	0.05	-	nuc	0					110
P01658 UniProt NPD GO	KV3F_MOUSE	Ig kappa chain V-III region MOPC 321 precursor	0.05	-	mit	0					132
P01661 UniProt NPD GO	KV3I_MOUSE	Ig kappa chain V-III region MOPC 63 precursor	0.05	-	mit	0					131
P01657 UniProt NPD GO	KV3E_MOUSE	Ig kappa chain V-III region PC 2413	0.05	-	mit	0					111
P01659 UniProt NPD GO	KV3G_MOUSE	Ig kappa chain V-III region TEPC 124	0.05	-	cyt	0					112
P03984 UniProt NPD GO	KAC6_RABIT	Ig kappa chain b5 variant C region	0.05	-	nuc	0					104
P01706 UniProt NPD GO	LV2C_HUMAN	Ig lambda chain V-II region BOH	0.05	-	nuc	0		extracellular region [NAS]			111
P01709 UniProt NPD GO	LV2F_HUMAN	Ig lambda chain V-II region MGC	0.05	-	nuc	0		extracellular region [NAS]		2MCG	111
P01721 UniProt NPD GO	LV6A_HUMAN	Ig lambda chain V-VI region AR	0.05	-	nuc	0		extracellular region [NAS]			112
P20766 UniProt NPD GO	LAC1_RAT	Ig lambda-1 chain C region	0.05	-	nuc	0					104
P01723 UniProt NPD GO	LV1A_MOUSE	Ig lambda-1 chain V region precursor	0.05	-	vac	0					117
O94303 UniProt NPD GO	HIS5_SCHPO	Imidazole glycerol phosphate synthase hisHF (IGP synthase) (ImGP synthase) (IGPS) [Includes: Glutami ...	0.05	-	cyt	0					541
P33734 UniProt NPD GO	HIS5_YEAST	Imidazole glycerol phosphate synthase hisHF (IGP synthase) (ImGP synthase) (IGPS) [Includes: Glutami ...	0.05	-	cyt	0		intracellular [TAS]		1OX6	552
Q75B47 UniProt NPD GO	HIS7_ASHGO	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.05	-	cyt	0					220
P28624 UniProt NPD GO	HIS7_PHYPR	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.05	-	cyt	0					452
P34048 UniProt NPD GO	HIS7_WHEAT	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD) (Fragment)	0.05	-	cyt	0					195
Q08749 UniProt NPD GO	TIM18_YEAST	Import inner membrane translocase subunit TIM18, mitochondrial precursor	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane protein insert... [IDA]			192
Q494P0 UniProt NPD GO	PHT17_ARATH	Inorganic phosphate transporter 1-7 (AtPht1;7) (H(+)/Pi cotransporter)	0.05	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)				535
Q9BY32 UniProt NPD GO	ITPA_HUMAN	Inosine triphosphate pyrophosphatase (EC 3.6.1.19) (ITPase) (Inosine triphosphatase) (Putative oncog ...	0.05	-	cyt	0	Cytoplasm		147520	2CAR	194
P50097 UniProt NPD GO	IMDH_TRIFO	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.05	-	cyt	0				1PVN	503
Q4V8T0 UniProt NPD GO	MIOX_BRARE	Inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase)	0.05	-	nuc	0	Cytoplasm (By similarity)				278
Q9UGB7 UniProt NPD GO	MIOX_HUMAN	Inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase) (Aldehyde reductase-like 6) (Renal-specif ...	0.05	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS] inclusion body [ISS]	606774		285
O64437 UniProt NPD GO	INO1_ORYSA	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.05	-	cyt	0	Cytoplasm (By similarity)				510
Q03529 UniProt NPD GO	SCS7_YEAST	Inositolphosphorylceramide-B C-26 hydroxylase (EC 1.-.-.-) (IPC-B hydroxylase)	0.05	-	end	3	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IMP]			384
P82812 UniProt NPD GO	SIX2_BUTSI	Insect toxin 2 (BsIT2) (Bs-dprIT2)	0.05	-	nuc	0	Secreted protein				61
P68726 UniProt NPD GO	SX25_LEIQH	Insect toxin 2-53 precursor (LqhIT2-53)	0.05	-	vac	0	Secreted protein				85
P67970 UniProt NPD GO	INS_CHICK	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.05	-	vac	0	Secreted protein				107
P30410 UniProt NPD GO	INS_PANTR	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.05	-	vac	0	Secreted protein				110
Q5XIE8 UniProt NPD GO	ITM2B_RAT	Integral membrane protein 2B	0.05	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				266
Q4V8X0 UniProt NPD GO	GP175_BRARE	Integral membrane protein GPR175	0.05	-	end	7	Membrane; multi-pass membrane protein (By similarity)				378

You are viewing entries 74701 to 74750 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.