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
Q9M3L4 UniProt NPD GO	CEMA_SPIOL	Chloroplast envelope membrane protein	0.11	-	end	2 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P09887 UniProt NPD GO	HS22C_SOYBN	Chloroplast small heat shock protein (Fragment)	0.11	-	cyt	0	Plastid; chloroplast				181
Q9Z0F5 UniProt NPD GO	CH25H_MOUSE	Cholesterol 25-hydroxylase (EC 1.14.99.38) (Cholesterol 25-monooxygenase) (m25OH)	0.11	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				298
Q8N4M1 UniProt NPD GO	CTL3_HUMAN	Choline transporter-like protein 3 (Solute carrier family 44 member 3)	0.11	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				653
Q921V7 UniProt NPD GO	CTL3_MOUSE	Choline transporter-like protein 3 (Solute carrier family 44 member 3)	0.11	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				652
Q03311 UniProt NPD GO	CHLE_MOUSE	Cholinesterase precursor (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylchol ...	0.11	-	exc	1 *					603
P13427 UniProt NPD GO	CH19_DROGR	Chorion protein S19	0.11	-	vac	1 *					196
P18121 UniProt NPD GO	CSH1_MOUSE	Chorionic somatomammotropin hormone 1 precursor (Placental lactogen I) (PL-I)	0.11	-	vac	0	Secreted protein				224
P14080 UniProt NPD GO	PAPA2_CARPA	Chymopapain precursor (EC 3.4.22.6) (Papaya proteinase II) (PPII)	0.11	-	mit	0				1YAL	352
P18276 UniProt NPD GO	CHYM_SHEEP	Chymosin precursor (EC 3.4.23.4) (Preprorennin)	0.11	-	end	0					381
P56682 UniProt NPD GO	AMCI_APIME	Chymotrypsin inhibitor (AMCI)	0.11	-	nuc	0	Secreted protein			1CCV	56
Q9LIG0 UniProt NPD GO	Y3136_ARATH	Clavaminate synthase-like protein At3g21360 (EC 1.-.-.-)	0.11	-	cyt	0				1Y0Z	330
Q14019 UniProt NPD GO	COTL1_HUMAN	Coactosin-like protein	0.11	-	cyt	0			606748	1WNJ	141
P35606 UniProt NPD GO	COPB2_HUMAN	Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP) (p102)	0.11	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]	606990		905
Q9YHV0 UniProt NPD GO	NXS4_NAJAT	Cobrotoxin IV (CBT IV)	0.11	-	nuc	0	Secreted protein (By similarity)				61
P80032 UniProt NPD GO	COLE_ZOPAT	Coleoptericin	0.11	-	nuc	0	Secreted protein				74
Q9D1D6 UniProt NPD GO	CTHR1_MOUSE	Collagen triple helix repeat-containing protein 1 precursor	0.11	-	exc	1 *	Secreted protein; extracellular space (By similarity)				245
O77656 UniProt NPD GO	MMP13_BOVIN	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)	0.11	-	exc	0					471
O35658 UniProt NPD GO	C1QBP_MOUSE	Complement component 1 Q subcomponent-binding protein, mitochondrial precursor (Glycoprotein gC1qBP) ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)	mitochondrion [IDA]			278
Q86RA3 UniProt NPD GO	CXO6A_CONVX	Conotoxin vx6a precursor	0.11	-	nuc	1 *	Secreted protein				74
Q5K0D3 UniProt NPD GO	CXO6_CONST	Conotoxin-6 precursor	0.11	-	exc	1 *	Secreted protein (By similarity)				77
Q62682 UniProt NPD GO	CNTN3_RAT	Contactin-3 precursor (Brain-derived immunoglobulin superfamily protein 1) (BIG-1)	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				1028
O14618 UniProt NPD GO	CCS_HUMAN	Copper chaperone for superoxide dismutase (Superoxide dismutase copper chaperone)	0.11	-	cyt	0	Cytoplasm	soluble fraction [TAS]	603864	2CRL	274
Q9WU84 UniProt NPD GO	CCS_MOUSE	Copper chaperone for superoxide dismutase (Superoxide dismutase copper chaperone)	0.11	-	cyt	0	Cytoplasm (By similarity)				274
Q9JK72 UniProt NPD GO	CCS_RAT	Copper chaperone for superoxide dismutase (Superoxide dismutase copper chaperone)	0.11	-	cyt	0	Cytoplasm (By similarity)				274
Q06686 UniProt NPD GO	CTR3_YEAST	Copper transport protein CTR3 (Copper transporter 3)	0.11	-	end	3 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			241
Q25588 UniProt NPD GO	CHH2_ORCLI	Crustacean hyperglycemic hormones A* precursor (CHH A) [Contains: CHH precursor-related peptide A ...	0.11	-	exc	1 *	Secreted protein				135
Q86GF7 UniProt NPD GO	CRUST_PANBO	Crustapain precursor (EC 3.4.22.-) (NsCys)	0.11	-	exc	0	Secreted protein	extracellular region [IC]			323
Q5IFN2 UniProt NPD GO	CRYD_OSTTA	Cryptochrome DASH, chloroplast/mitochondrial precursor	0.11	-	cyt	0	Plastid; chloroplast (Potential). Mitochondrion (By similarity)				546
P15968 UniProt NPD GO	TXC3_HOLCU	Curtatoxin-3 (CT-III)	0.11	-	nuc	0	Secreted protein				38
P81577 UniProt NPD GO	CUPA3_CANPG	Cuticle protein AM1199 (CPAM1199)	0.11	-	nuc	0					108
P00590 UniProt NPD GO	CUTI1_FUSSO	Cutinase-1 precursor (EC 3.1.1.74) (Cutin hydrolase 1)	0.11	-	exc	0	Secreted protein			2CUT	230
P23404 UniProt NPD GO	RR17_CYAPA	Cyanelle 30S ribosomal protein S17	0.11	-	nuc	0	Plastid; cyanelle				88
P14807 UniProt NPD GO	RK5_CYAPA	Cyanelle 50S ribosomal protein L5	0.11	-	cyt	0	Plastid; cyanelle				181
P14808 UniProt NPD GO	RK6_CYAPA	Cyanelle 50S ribosomal protein L6	0.11	-	mit	0	Plastid; cyanelle				179
O76096 UniProt NPD GO	CYTF_HUMAN	Cystatin F precursor (Leukocystatin) (Cystatin-7) (Cystatin-like metastasis-associated protein) (CMA ...	0.11	-	exc	0	Secreted protein. Cytoplasm		603253	2CH9	145
P53867 UniProt NPD GO	ATG4_YEAST	Cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.11	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] cytosol [IDA] microtubule associated complex [IPI]			494
P54640 UniProt NPD GO	CYSP5_DICDI	Cysteine proteinase 5 precursor (EC 3.4.22.-)	0.11	-	exc	0	Lysosome				344
P47999 UniProt NPD GO	CYSKP_ARATH	Cysteine synthase, chloroplast precursor (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserin ...	0.11	-	mit	0	Plastid; chloroplast; chloroplast stroma. Plastid; chromoplast				392
Q03401 UniProt NPD GO	CRIS1_MOUSE	Cysteine-rich secretory protein 1 precursor (CRISP-1) (Acidic epididymal glycoprotein 1) (Sperm-coat ...	0.11	-	exc	0	Stored in secretory granules of granular convoluted tubules cells				244
Q64410 UniProt NPD GO	CP17A_CAVPO	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.11	-	nuc	0					508
P33272 UniProt NPD GO	CP2BC_RAT	Cytochrome P450 2B12 (EC 1.14.14.1) (CYPIIB12)	0.11	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
O62671 UniProt NPD GO	CP241_CANFA	Cytochrome P450 2C41 (EC 1.14.14.1) (CYPIIC41)	0.11	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				489
P10633 UniProt NPD GO	CP2D1_RAT	Cytochrome P450 2D1 (EC 1.14.14.1) (CYPIID1) (P450-DB1) (P450-CMF1A) (P450-UT-7) (Debrisoquine 4-hyd ...	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
P12938 UniProt NPD GO	CP2D3_RAT	Cytochrome P450 2D3 (EC 1.14.14.1) (CYPIID3) (P450-DB3) (Debrisoquine 4-hydroxylase)	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
Q6VVW9 UniProt NPD GO	CP2R1_MOUSE	Cytochrome P450 2R1 (EC 1.14.14.-) (Vitamin D 25-hydroxylase)	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				501
P79152 UniProt NPD GO	CP3AJ_CAPAE	Cytochrome P450 3A19 (EC 1.14.14.1) (CYPIIIA19) (Fragment)	0.11	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				218
P58049 UniProt NPD GO	C71BB_ARATH	Cytochrome P450 71B11 (EC 1.14.-.-)	0.11	-	nuc	1 *					496
Q9LW27 UniProt NPD GO	C71BF_ARATH	Cytochrome P450 71B15 (EC 1.14.-.-)	0.11	-	mit	1 *					490
O48958 UniProt NPD GO	C71E1_SORBI	Cytochrome P450 71E1 (EC 1.14.13.68) (4-hydroxyphenylacetaldehyde oxime monooxygenase)	0.11	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				531

You are viewing entries 62501 to 62550 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.