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
P12097 UniProt NPD GO	RK23_ORYSA	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93
Q6L3C0 UniProt NPD GO	RK23_SACHY	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93
Q6ENR9 UniProt NPD GO	RK23_SACOF	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93
P69667 UniProt NPD GO	RK23_WHEAT	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93
P51303 UniProt NPD GO	RK24_PORPU	Chloroplast 50S ribosomal protein L24	0.04	-	nuc	0	Plastid; chloroplast				95
P41548 UniProt NPD GO	RK27_CALSH	Chloroplast 50S ribosomal protein L27 (Fragment)	0.04	-	cyt	0	Plastid; chloroplast				74
P41550 UniProt NPD GO	RK27_CHRHI	Chloroplast 50S ribosomal protein L27 (Fragment)	0.04	-	cyt	0	Plastid; chloroplast				73
P41553 UniProt NPD GO	RK27_PORCR	Chloroplast 50S ribosomal protein L27 (Fragment)	0.04	-	nuc	0	Plastid; chloroplast				47
P41551 UniProt NPD GO	RK2X_CYACA	Chloroplast 50S ribosomal protein L27 (Fragment)	0.04	-	mit	0	Plastid; chloroplast				47
Q6B8V3 UniProt NPD GO	RK3_GRATL	Chloroplast 50S ribosomal protein L3	0.04	-	cyt	0	Plastid; chloroplast				205
Q71E53 UniProt NPD GO	CEMA_FAGSY	Chloroplast envelope membrane protein	0.04	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
Q68RZ4 UniProt NPD GO	CEMA_PANGI	Chloroplast envelope membrane protein	0.04	-	vac	3 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P46559 UniProt NPD GO	KICB2_CAEEL	Choline kinase B2 (EC 2.7.1.32)	0.04	-	cyt	0					369
Q95JW2 UniProt NPD GO	CTL5_MACFA	Choline transporter-like protein 5 (Solute carrier family 44 member 5)	0.04	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				717
Q95001 UniProt NPD GO	CHLE2_BRALA	Cholinesterase 2 (EC 3.1.1.8) (Fragment)	0.04	-	cyt	0					337
P17404 UniProt NPD GO	LECT1_BOVIN	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) (Small c ...	0.04	-	cyt	1 *	Cytoplasm. Secreted protein. Accumulated in the inter-territorial matrix of cartilage				335
O75829 UniProt NPD GO	LECT1_HUMAN	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) [Contain ...	0.04	-	cyt	1 *	Cytoplasm. Secreted protein. Accumulated in the inter-territorial matrix of cartilage		605147		334
Q9Z1F6 UniProt NPD GO	LECT1_MOUSE	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) [Contain ...	0.04	-	cyt	1 *	Cytoplasm (By similarity). Secreted protein (By similarity). Accumulated in the inter-territorial ma ...				334
P05686 UniProt NPD GO	CHE1_ANTPO	Chorion E1 protein precursor	0.04	-	exc	0					169
P13424 UniProt NPD GO	CH15_DROVI	Chorion protein S15	0.04	-	vac	0					116
P24515 UniProt NPD GO	CH18_DROVI	Chorion protein S18	0.04	-	mit	0					170
Q9DFZ4 UniProt NPD GO	CHUR_XENLA	Churchill protein	0.04	-	cyt	0					112
P84310 UniProt NPD GO	CTR1_LUMTE	Chymotrypsin LT_CH 1 (EC 3.4.21.1) (Fragment)	0.04	-		0	Secreted protein; extracellular space (By similarity)				19
P04813 UniProt NPD GO	CTR2_CANFA	Chymotrypsinogen 2 precursor (EC 3.4.21.1) [Contains: Chymotrypsin 2 chain A; Chymotrypsin 2 chain B ...	0.04	-	end	1 *	Secreted protein; extracellular space				263
P00767 UniProt NPD GO	CTRB_BOVIN	Chymotrypsinogen B (EC 3.4.21.1) [Contains: Chymotrypsin B chain A; Chymotrypsin B chain B; Chymotry ...	0.04	-	cyt	0	Secreted protein; extracellular space			1HJA	245
P07338 UniProt NPD GO	CTRB1_RAT	Chymotrypsinogen B precursor (EC 3.4.21.1) [Contains: Chymotrypsin B chain A; Chymotrypsin B chain B ...	0.04	-	end	1 *	Secreted protein; extracellular space			1KDQ	263
P51641 UniProt NPD GO	CNTFR_CHICK	Ciliary neurotrophic factor receptor alpha precursor (CNTFR alpha) (Growth-promoting activity recept ...	0.04	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				362
Q5E9L0 UniProt NPD GO	CLD10_BOVIN	Claudin-10	0.04	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				231
Q5R8E5 UniProt NPD GO	CLD10_PONPY	Claudin-10	0.04	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein				228
P78369 UniProt NPD GO	CLD10_HUMAN	Claudin-10 (OSP-like protein)	0.04	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			228
Q9Z0S3 UniProt NPD GO	CLD14_MOUSE	Claudin-14	0.04	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			239
P17698 UniProt NPD GO	CLUS_SHEEP	Clusterin (Sulfated glycoprotein 2) (SGP-2) [Contains: Clusterin beta chain; Clusterin alpha chain] ...	0.04	-	cyt	0	Secreted protein				66
P00741 UniProt NPD GO	FA9_BOVIN	Coagulation factor IX (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa light chai ...	0.04	-	nuc	0	Secreted protein			1J35	416
Q804X6 UniProt NPD GO	FA9_CHICK	Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa ...	0.04	-	cyt	0	Secreted protein (By similarity)				471
P12260 UniProt NPD GO	F13A_BOVIN	Coagulation factor XIII A chain precursor (EC 2.3.2.13) (Coagulation factor XIIIa) (Protein-glutamin ...	0.04	-	nuc	0	Cytoplasm. Secreted protein. Secreted into the blood plasma. Cytoplasmic in most tissues, but also s ...				37
P78929 UniProt NPD GO	COFI_SCHPO	Cofilin	0.04	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)	actin cortical patch [TAS]			137
Q07202 UniProt NPD GO	CORA_MEDSA	Cold and drought-regulated protein CORA	0.04	-	exc	0					204
P50454 UniProt NPD GO	SPH2_HUMAN	Collagen-binding protein 2 precursor (Colligin 2) (Rheumatoid arthritis-related antigen RA-A47) (Ser ...	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [NAS] ER-Golgi intermediate compartment [IDA]	600943		418
O18927 UniProt NPD GO	MMP13_HORSE	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)	0.04	-	exc	0					472
P09871 UniProt NPD GO	C1S_HUMAN	Complement C1s subcomponent precursor (EC 3.4.21.42) (C1 esterase) [Contains: Complement C1s subcomp ...	0.04	-	vac	0			120580	1NZI	688
Q3T0B6 UniProt NPD GO	C1QBP_BOVIN	Complement component 1 Q subcomponent-binding protein, mitochondrial precursor	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				278
P03953 UniProt NPD GO	CFAD_MOUSE	Complement factor D precursor (EC 3.4.21.46) (C3 convertase activator) (Properdin factor D) (Adipsin ...	0.04	-	exc	0	Secreted protein	extracellular space [IDA]			259
O42636 UniProt NPD GO	CIA30_NEUCR	Complex I intermediate-associated protein 30, mitochondrial precursor	0.04	-	cyt	0	Mitochondrion	respiratory chain complex I (sensu Eukaryota) [IDA]			278
P34762 UniProt NPD GO	CON6_NEUCR	Conidiation-specific protein 6	0.04	-	nuc	0					93
P0C1N2 UniProt NPD GO	CXM33_CONMR	Conotoxin Mr3.3 precursor	0.04	-	exc	0	Secreted protein (By similarity)				68
P58842 UniProt NPD GO	CX3B_CONQU	Conotoxin QcIIIB	0.04	-		0	Secreted protein				15
P0C1M8 UniProt NPD GO	CXO7A_CONRA	Conotoxin r7a precursor (Light sleeper) (Fragment)	0.04	-	cyt	0	Secreted protein				38
Q5K0D6 UniProt NPD GO	CXO12_CONST	Conotoxin-12 precursor	0.04	-	exc	1 *	Secreted protein (By similarity)				78
Q5K0D8 UniProt NPD GO	CXO2_CONST	Conotoxin-2 precursor	0.04	-	exc	1 *	Secreted protein (By similarity)				78
P58784 UniProt NPD GO	COW1_CONPU	Contryphan-P precursor	0.04	-	exc	0	Secreted protein				63

You are viewing entries 76551 to 76600 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.