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
P0C030 UniProt NPD GO	RUB1_ORYSA	NEDD8-like protein RUB1 precursor (Ubiquitin-related protein 1) (OsRUB1)	0.05	-	cyt	0					77
P0C032 UniProt NPD GO	RUB3_ORYSA	NEDD8-like protein RUB3 precursor (Ubiquitin-related protein 3) (OsRUB3)	0.05	-	cyt	0					78
Q6VVB1 UniProt NPD GO	NHLC1_HUMAN	NHL repeat-containing protein 1 (Malin)	0.05	-	cyt	0	Endoplasmic reticulum. Nucleus. Localizes at the endoplasmic reticulum and, to a lesser extent, in t ...		608072		395
Q8BGN5 UniProt NPD GO	NPAL3_MOUSE	NIPA-like protein 3	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				410
Q05963 UniProt NPD GO	FL3H_CALCH	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT)	0.05	-	cyt	0					356
Q94518 UniProt NPD GO	NACA_DROME	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.05	-	cyt	0					217
P60589 UniProt NPD GO	NWAP_NAJNG	Nawaprin	0.05	-	nuc	0	Secreted protein			1UDK	51
Q9UR17 UniProt NPD GO	NRF1_SCHPO	Negative regulator of cdc42	0.05	-	end	3 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane [IDA]			122
Q6FKD4 UniProt NPD GO	PHO85_CANGA	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85)	0.05	-	cyt	0					302
Q92241 UniProt NPD GO	PHO85_KLULA	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85)	0.05	-	cyt	0					304
Q90W04 UniProt NPD GO	NGB_TETNG	Neuroglobin	0.05	-	cyt	0					159
Q9HB89 UniProt NPD GO	NMUR1_HUMAN	Neuromedin U receptor 1 (NMU-R1) (G-protein coupled receptor 66) (G-protein coupled receptor FM-3)	0.05	+	end	7	Membrane; multi-pass membrane protein	integral to membrane [IDA] membrane fraction [IDA]	604153		426
P20056 UniProt NPD GO	NEUU_RANTE	Neuromedin U-25 (NmU-25)	0.05	-	cyt	0	Secreted protein				25
P34966 UniProt NPD GO	NEUU_CAVPO	Neuromedin U-9 (NmU-9)	0.05	-		0	Secreted protein				9
P09481 UniProt NPD GO	ACHA3_CHICK	Neuronal acetylcholine receptor protein subunit alpha-3 precursor	0.05	-	end	4	Membrane; multi-pass membrane protein				496
Q8R4G9 UniProt NPD GO	ACHA3_MOUSE	Neuronal acetylcholine receptor protein subunit alpha-3 precursor	0.05	-	end	4	Membrane; multi-pass membrane protein (By similarity)				499
P43143 UniProt NPD GO	ACHA6_RAT	Neuronal acetylcholine receptor protein subunit alpha-6 precursor	0.05	-	end	4	Membrane; multi-pass membrane protein				493
Q90667 UniProt NPD GO	NP311_CHICK	Neuronal protein 3.1 (P311 protein)	0.05	-	cyt	0					68
Q63447 UniProt NPD GO	NPY4R_RAT	Neuropeptide Y receptor type 4 (NPY4-R) (Pancreatic polypeptide receptor 1) (PP1)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				375
Q61041 UniProt NPD GO	NPY4R_MOUSE	Neuropeptide Y receptor type 4 (NPY4-R) (Pancreatic polypeptide receptor 1) (PP1) (NPYR-D)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				375
Q95ZN4 UniProt NPD GO	NLP33_CAEEL	Neuropeptide-like protein 33 precursor	0.05	-	vac	1 *	Secreted protein (Potential)				74
P15228 UniProt NPD GO	AEP1_MESMA	Neurotoxin AEP precursor (Anti-epilepsy peptide) (BmK AEP)	0.05	-	exc	0	Secreted protein	extracellular region [IDA]			85
P83400 UniProt NPD GO	SCX3_MESTA	Neurotoxin BtITx3 precursor (Neurotoxin BTChl1)	0.05	-	mit	0	Secreted protein	extracellular region [NAS]			60
P59355 UniProt NPD GO	SCX2_LEIQH	Neurotoxin Lqh II (LqhII) (Lqh2)	0.05	-	nuc	0	Secreted protein				64
P01498 UniProt NPD GO	SCXP_ANDMA	Neurotoxin P2	0.05	-	nuc	0	Secreted protein				35
P83896 UniProt NPD GO	TX28_PHOKE	Neurotoxin PKTx28C4	0.05	-	nuc	0	Secreted protein				38
P83903 UniProt NPD GO	TX18_PHORI	Neurotoxin PRTx18C2 (Fragment)	0.05	-	nuc	0	Secreted protein				54
P83904 UniProt NPD GO	TX32_PHORI	Neurotoxin PRTx32C1	0.05	-	nuc	0	Secreted protein				47
P46066 UniProt NPD GO	SCXV_CENSC	Neurotoxin V (CsE-V) (CsEV) (B140-1)	0.05	-	nuc	0	Secreted protein			1NRB	63
P83562 UniProt NPD GO	TXMG6_MACGS	Neurotoxin magi-6 precursor	0.05	-	exc	1 *	Secreted protein				82
P45668 UniProt NPD GO	SCX2_MESTA	Neurotoxin-2 (Neurotoxin II) (BT-II) (Fragment)	0.05	-	nuc	0	Secreted protein				24
P30785 UniProt NPD GO	TXA5_RADMA	Neurotoxin-5 (Toxin RTX-V)	0.05	-	nuc	0	Secreted protein. Found in nematocyst				47
Q7ZT13 UniProt NPD GO	NXLW_BUNMU	Neurotoxin-like protein pMD18-NTL1/2/4/5 precursor	0.05	-	exc	0	Secreted protein				86
Q55G11 UniProt NPD GO	NCSEB_DICDI	Neutral ceramidase B precursor (EC 3.5.1.23) (NCDase B) (N-CDase B) (Acylsphingosine deacylase 2B) ( ...	0.05	-	end	1 *	Secreted protein (Potential)				718
Q9NZG7 UniProt NPD GO	NINJ2_HUMAN	Ninjurin-2 (Nerve injury-induced protein 2)	0.05	-	end	2	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607297		142
P07857 UniProt NPD GO	NLTP_BOVIN	Nonspecific lipid-transfer protein (EC 2.3.1.176) (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol ...	0.05	-	pox	0	Cytoplasm. Mitochondrion. Cytoplasmic in the liver and also associated with mitochondria especially ...				543
P22307 UniProt NPD GO	NLTP_HUMAN	Nonspecific lipid-transfer protein (EC 2.3.1.176) (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol ...	0.05	-	pox	0	Cytoplasm. Mitochondrion. Isoform SCPx: Peroxisome. Cytoplasmic in the liver and also associated wit ...	peroxisome [TAS]	184755	1QND	547
O62742 UniProt NPD GO	NLTP_RABIT	Nonspecific lipid-transfer protein (EC 2.3.1.176) (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol ...	0.05	-	pox	0	Cytoplasm (By similarity). Mitochondrion (By similarity). Isoform SCPx: Peroxisome (By similarity). ...			1C44	547
P23096 UniProt NPD GO	NLTP1_ORYSA	Nonspecific lipid-transfer protein 1 precursor (LTP 1) (PAPI)	0.05	-	exc	1 *				1UVC	116
O65091 UniProt NPD GO	NLTP4_ORYSA	Nonspecific lipid-transfer protein 4 precursor (LTP 4)	0.05	-	exc	1 *					119
Q43767 UniProt NPD GO	NLT41_HORVU	Nonspecific lipid-transfer protein 4.1 precursor (LTP 4.1) (CW21) (CW-21)	0.05	-	exc	1 *					115
P10974 UniProt NPD GO	NLTPB_RICCO	Nonspecific lipid-transfer protein B (NS-LTP B) (Phospholipid transfer protein) (PLTP)	0.05	-	nuc	0					92
Q43871 UniProt NPD GO	NLTP8_HORVU	Nonspecific lipid-transfer protein Cw18 precursor (LTP Cw-18) (PKG2316)	0.05	-	exc	1 *					115
Q00049 UniProt NPD GO	NORA_ASPFL	Norsolorinic acid reductase (EC 1.1.1.-)	0.05	-	cyt	0					388
Q00258 UniProt NPD GO	NORA_ASPPA	Norsolorinic acid reductase (EC 1.1.1.-)	0.05	-	cyt	0					388
Q10099 UniProt NPD GO	SEH1_SCHPO	Nuclear pore protein SEH1 homolog	0.05	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (Potential)	Nup107-160 complex [IDA]			339
P60193 UniProt NPD GO	RNZN_WHEAT	Nuclear ribonuclease Z (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease) (Zinc phosphodieste ...	0.05	-	cyt	0	Nucleus (Probable)				176
Q6Z348 UniProt NPD GO	NFYB1_ORYSA	Nuclear transcription factor Y subunit B-1 (OsNF-YB-1) (CCAAT-binding transcription factor subunit N ...	0.05	-	cyt	0	Nucleus (Probable)				186
Q4PSE2 UniProt NPD GO	NFYC8_ARATH	Nuclear transcription factor Y subunit C-8 (AtNF-YC-8)	0.05	-	nuc	0	Nucleus (By similarity)				187
Q96VN3 UniProt NPD GO	NTF2_EMENI	Nuclear transport factor 2 (NTF-2)	0.05	-	cyt	0	Cytoplasm (By similarity)				125

You are viewing entries 75001 to 75050 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.