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
P56745 UniProt NPD GO	CLD1_RAT	Claudin-1	0.06	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] lateral plasma membrane [IDA] tight junction [ISS]			211
O95832 UniProt NPD GO	CLD1_HUMAN	Claudin-1 (Senescence-associated epithelial membrane protein)	0.06	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS] tight junction [ISS]	603718		211
Q2KIY2 UniProt NPD GO	CLD15_BOVIN	Claudin-15	0.06	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				235
P56880 UniProt NPD GO	CLD20_HUMAN	Claudin-20	0.06	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			219
Q8N7P3 UniProt NPD GO	CLD22_HUMAN	Claudin-22	0.06	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			220
P28707 UniProt NPD GO	SBA1_YEAST	Co-chaperone protein SBA1	0.06	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		2CG9	215
P03998 UniProt NPD GO	COAG_LIMPO	Coagulogen precursor [Contains: Coagulin chain A; Peptide C; Coagulin chain B]	0.06	-	exc	0	Secreted protein				195
P40765 UniProt NPD GO	COPA_CANFA	Coatomer subunit alpha (Alpha-coat protein) (Alpha-COP) (HEPCOP) (HEP-COP) [Contains: Xenin (Xenopsi ...	0.06	-	cyt	0					35
Q9P299 UniProt NPD GO	COPZ2_HUMAN	Coatomer subunit zeta-2 (Zeta-2 coat protein) (Zeta-2 COP)	0.06	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [NAS] Golgi cis-face [NAS]			210
P11148 UniProt NPD GO	COL_CHICK	Colipase (Fragment)	0.06	-	nuc	0	Secreted protein				34
P17084 UniProt NPD GO	COL_RAT	Colipase precursor	0.06	-	exc	1 *	Secreted protein				112
P31720 UniProt NPD GO	C1QA_RAT	Complement C1q subcomponent subunit A precursor	0.06	-	mit	0	Secreted protein				245
Q9BXJ5 UniProt NPD GO	C1QT2_HUMAN	Complement C1q tumor necrosis factor-related protein 2 precursor	0.06	-	vac	0	Secreted protein (Potential)				285
Q9BXJ0 UniProt NPD GO	C1QT5_HUMAN	Complement C1q tumor necrosis factor-related protein 5 precursor	0.06	-	exc	0	Secreted protein (Probable)		608752		243
Q6P6T1 UniProt NPD GO	C1S_RAT	Complement C1s subcomponent precursor (EC 3.4.21.42) (C1 esterase) [Contains: Complement C1s subcomp ...	0.06	-	end	0		extracellular region [IDA]			688
Q8CG14 UniProt NPD GO	CS1A_MOUSE	Complement C1s-A subcomponent precursor (EC 3.4.21.42) (C1 esterase) [Contains: Complement C1s-A sub ...	0.06	-	exc	0					688
P51779 UniProt NPD GO	CFAD_PIG	Complement factor D precursor (EC 3.4.21.46) (C3 convertase activator) (Properdin factor D) (Adipsin ...	0.06	-	end	0	Secreted protein				259
P81461 UniProt NPD GO	CONA_CANVI	Concanavalin A (Con A)	0.06	-	cyt	0				2A7A	237
P02866 UniProt NPD GO	CONA_CANEN	Concanavalin A precursor (Con A)	0.06	-	exc	1 *				5CNA	290
P55915 UniProt NPD GO	CONA_CANBR	Concanavalin BR (Con BR)	0.06	-	cyt	0				1QDO	237
P19463 UniProt NPD GO	CON13_NEUCR	Conidiation-specific protein 13	0.06	-	exc	0					340
Q9TWL9 UniProt NPD GO	COMA_CONMA	Conodipine-M alpha chain (EC 3.1.1.4)	0.06	-	nuc	0	Secreted protein				77
P84197 UniProt NPD GO	CX11_CONRE	Conotoxin Rg11a	0.06	-	nuc	0	Secreted protein				44
P0C1M9 UniProt NPD GO	CXM3A_CONMR	Conotoxin mr3a	0.06	-		0	Secreted protein				17
P0C1N0 UniProt NPD GO	CXM3B_CONMR	Conotoxin mr3b	0.06	-		0	Secreted protein				19
P58846 UniProt NPD GO	CXM3C_CONTE	Conotoxin tx3c precursor (Conotoxin Tx3.4) (Textile scratcher peptide)	0.06	-	exc	0	Secreted protein				65
Q5K0C0 UniProt NPD GO	CXO3_CONIM	Conotoxin-3 precursor	0.06	+	exc	2 *	Secreted protein (By similarity)				81
Q5K0C1 UniProt NPD GO	CXO5_CONIM	Conotoxin-5 precursor	0.06	+	vac	1 *	Secreted protein (By similarity)				78
Q5K0C2 UniProt NPD GO	CXO6_CONIM	Conotoxin-6 precursor	0.06	+	vac	1 *	Secreted protein (By similarity)				78
Q9LJD7 UniProt NPD GO	COP10_ARATH	Constitutive photomorphogenesis protein 10	0.06	-	mit	0	Nucleus				182
Q9USV7 UniProt NPD GO	CTR6_SCHPO	Copper transport protein ctr6 (Copper transporter 6)	0.06	-	end	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein				148
Q9U620 UniProt NPD GO	MTCU_CALSI	Copper-specific metallothionein-2 (CuMT-II)	0.06	-	nuc	0					64
O19084 UniProt NPD GO	CDSN_PIG	Corneodesmosin (S protein) (Fragment)	0.06	-	nuc	0	Secreted protein. Found in corneodesmosomes, the intercellular structures that are involved in desqu ...				225
Q9BR76 UniProt NPD GO	COR1B_HUMAN	Coronin-1B (Coronin-2)	0.06	-	nuc	0	Localized to the leading edge in fibroblasts, as well as weakly along actin stress fibers		609849		489
Q9XS70 UniProt NPD GO	COR1B_RABIT	Coronin-1B (Coroninse) (Coronin-like protein pp66)	0.06	-	nuc	0	Localized to the leading edge in fibroblasts, as well as weakly along actin stress fibers (By simila ...				486
P50172 UniProt NPD GO	DHI1_MOUSE	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.06	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein			1Y5R	291
Q6R0J2 UniProt NPD GO	DHI1_MESAU	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.06	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				291
P24722 UniProt NPD GO	KCRT_ONCMY	Creatine kinase, testis isozyme (EC 2.7.3.2)	0.06	-	cyt	0					383
O15981 UniProt NPD GO	CHH5_PENJP	Crustacean hyperglycemic hormones 5 precursor (Pej-SGP-V) [Contains: CHH precursor-related peptide 5 ...	0.06	-	exc	1 *	Secreted protein				125
Q25154 UniProt NPD GO	CHHB_HOMAM	Crustacean hyperglycemic hormones isoform B precursor [Contains: CHH precursor-related peptide B (CP ...	0.06	-	cyt	0	Secreted protein				134
Q25683 UniProt NPD GO	CHH_PROCL	Crustacean hyperglycemic hormones precursor [Contains: CHH precursor-related peptide (CPRP); Crustac ...	0.06	-	end	1 *	Secreted protein				137
P83352 UniProt NPD GO	CU16D_LIMPO	Cuticle protein 16 isoform D (LpCP16d) (Fragment)	0.06	-	nuc	0					59
P84252 UniProt NPD GO	CU168_IXORI	Cuticle protein 16.8 (Ir-ACP16.8)	0.06	-	nuc	0					161
P80233 UniProt NPD GO	CU67B_LOCMI	Cuticle protein 67, isoform B (LM-67B) (LM-ACP 67B)	0.06	-	cyt	0					104
P81578 UniProt NPD GO	CUPA4_CANPG	Cuticle protein AM1239 (CPAM1239)	0.06	-	cyt	0					112
P29292 UniProt NPD GO	CUTI_ASCRA	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.06	-	end	0	Secreted protein				223
Q96UT0 UniProt NPD GO	CUTI2_FUSSO	Cutinase-2 precursor (EC 3.1.1.74) (Cutin hydrolase 2)	0.06	-	exc	0	Secreted protein				231
Q96US9 UniProt NPD GO	CUTI3_FUSSO	Cutinase-3 precursor (EC 3.1.1.74) (Cutin hydrolase 3)	0.06	-	exc	0	Secreted protein				231
P34907 UniProt NPD GO	CAR2_DICDI	Cyclic AMP receptor 2 (cAMP receptor 2)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				375
O04147 UniProt NPD GO	CPD_ARATH	Cyclic phosphodiesterase (EC 3.1.4.-) (CPDase)	0.06	-	cyt	0	Cytoplasm	cytoplasm [IDA]		1JH7	181

You are viewing entries 71801 to 71850 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.