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
P24511 UniProt NPD GO	CH16_DROSU	Chorion protein S16	0.00	-	exc	0					141
P09873 UniProt NPD GO	CHYM_FELCA	Chymosin precursor (EC 3.4.23.4) (Fragment)	0.00	-	cyt	0					54
P35002 UniProt NPD GO	CTRP_PENMO	Chymotrypsin (EC 3.4.21.1) (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				31
P36178 UniProt NPD GO	CTRB2_PENVA	Chymotrypsin BII precursor (EC 3.4.21.1)	0.00	-	exc	0	Secreted protein; extracellular space				271
P83830 UniProt NPD GO	ICI_EISHO	Chymotrypsin inhibitor (EHCI) (Fragment)	0.00	-	cyt	0					41
P83472 UniProt NPD GO	ICI_LUMTE	Chymotrypsin inhibitor precursor (LTCI)	0.00	-	exc	0	Secreted protein				86
Q27289 UniProt NPD GO	CTR1_ANOGA	Chymotrypsin-1 precursor (EC 3.4.21.1)	0.00	-	end	0					259
P34168 UniProt NPD GO	LCLP_HUMAN	Chymotrypsin-like serine proteinase (EC 3.4.21.-) (LCLP) (Fragment)	0.00	-	cyt	0					26
P84642 UniProt NPD GO	CIRD_CHAPA	Circulin-D (CIRD)	0.00	-	nuc	0					30
P84643 UniProt NPD GO	CIRE_CHAPA	Circulin-E (CIRE)	0.00	-	nuc	0					30
P81835 UniProt NPD GO	CT11_LITCI	Citropin-1.1 [Contains: Citropin-1.1.1; Citropin-1.1.2]	0.00	-		0	Secreted protein				16
P81838 UniProt NPD GO	CT113_LITCI	Citropin-1.1.3	0.00	-		0	Secreted protein				18
P81840 UniProt NPD GO	CT12_LITCI	Citropin-1.2 [Contains: Citropin-1.2.1; Citropin-1.2.2; Citropin-1.2.3]	0.00	-		0	Secreted protein				16
P81844 UniProt NPD GO	CT124_LITCI	Citropin-1.2.4	0.00	-		0	Secreted protein				18
P81846 UniProt NPD GO	CT13_LITCI	Citropin-1.3	0.00	-		0	Secreted protein				16
P81847 UniProt NPD GO	CT21_LITCI	Citropin-2.1.3 [Contains: Citropin-2.1.2; Citropin-2.1.1; Citropin-2.1]	0.00	-	cyt	0	Secreted protein				26
P81851 UniProt NPD GO	CT31_LITCI	Citropin-3.1.2 [Contains: Citropin-3.1.1; Citropin-3.1]	0.00	-	cyt	0	Secreted protein				24
P28078 UniProt NPD GO	2DMA_MOUSE	Class II histocompatibility antigen, M alpha chain precursor	0.00	-	nuc	1	Endosome; late endosome; late endosomal membrane; single-pass type I membrane protein. Lysosome; lys ...	endosome membrane [IDA] intracellular [IDA] lysosomal membrane [IDA] multivesicular body [IDA]		1K8I	261
Q43560 UniProt NPD GO	PR1_MEDSA	Class-10 pathogenesis-related protein 1 (MSPR10-1)	0.00	-	cyt	0	Cytoplasm				157
Q9Z0S4 UniProt NPD GO	CLD13_MOUSE	Claudin-13	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein				211
P56746 UniProt NPD GO	CLD15_HUMAN	Claudin-15	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			228
Q9Z0S5 UniProt NPD GO	CLD15_MOUSE	Claudin-15	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			227
Q9XT98 UniProt NPD GO	CLD16_BOVIN	Claudin-16 (CL-16)	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			254
Q2HJ22 UniProt NPD GO	CLD5_BOVIN	Claudin-5	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				218
O54942 UniProt NPD GO	CLD5_MOUSE	Claudin-5 (Brain endothelial cell clone 1 protein) (Lung-specific membrane protein)	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			218
O00501 UniProt NPD GO	CLD5_HUMAN	Claudin-5 (Transmembrane protein deleted in VCFS) (TMDVCF)	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]	602101		218
Q3B7N4 UniProt NPD GO	CLD7_BOVIN	Claudin-7	0.00	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				211
P80710 UniProt NPD GO	CLAVA_STYCL	Clavanin-A precursor	0.00	-	exc	0	Secreted protein				80
O18493 UniProt NPD GO	CLAVC_STYCL	Clavanin-C precursor	0.00	-	vac	0	Secreted protein				80
P80713 UniProt NPD GO	CLAVD_STYCL	Clavanin-D precursor	0.00	-	exc	0	Secreted protein				80
O18492 UniProt NPD GO	CLAVE_STYCL	Clavanin-E precursor	0.00	-	exc	0	Secreted protein				80
O97395 UniProt NPD GO	CLAPI_STYCL	Clavaspirin precursor	0.00	-	exc	0	Secreted protein				80
P25692 UniProt NPD GO	KRCL_CHICK	Claw keratin (C-ker) (cKer)	0.00	-	cyt	0					127
P16291 UniProt NPD GO	FA9_SHEEP	Coagulation factor IX (EC 3.4.21.22) (Christmas factor) (Fragment)	0.00	-	cyt	0	Secreted protein				274
P23806 UniProt NPD GO	IXA_TRIFL	Coagulation factor IX/factor X-binding protein A chain precursor (IX/X-BP)	0.00	-	exc	0	Secreted protein			1J35	152
P84552 UniProt NPD GO	COCH_CAVPO	Cochlin (COCH-5B2) (Fragments)	0.00	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				35
P35586 UniProt NPD GO	COCO_LIMPO	Cocoonase (EC 3.4.21.-) (Fragment)	0.00	-		0	Secreted protein; extracellular space				14
P02704 UniProt NPD GO	COLA_HORSE	Colipase A precursor (Fragment)	0.00	-	exc	0	Secreted protein				106
P02705 UniProt NPD GO	COLB_HORSE	Colipase B precursor (Fragment)	0.00	-	exc	0	Secreted protein				108
P02703 UniProt NPD GO	COL_PIG	Colipase precursor (Procolipase II)	0.00	-	exc	0	Secreted protein			1PCO	112
P81609 UniProt NPD GO	COG2_CARMA	Collagenolytic protease (EC 3.4.21.32) (CSC) (Fragment)	0.00	-		0	Secreted protein; extracellular space				17
P34153 UniProt NPD GO	COG1_CHIOP	Collagenolytic protease 25 kDa II/III (EC 3.4.21.32) (Fragment)	0.00	-		0					20
P20731 UniProt NPD GO	COG1_PARCM	Collagenolytic protease 28 kDa (EC 3.4.21.32) (Fragment)	0.00	-		0					20
P14106 UniProt NPD GO	C1QB_MOUSE	Complement C1q subcomponent subunit B precursor	0.00	-	exc	0	Secreted protein				253
P31721 UniProt NPD GO	C1QB_RAT	Complement C1q subcomponent subunit B precursor	0.00	-	exc	0	Secreted protein	complement component C1q complex [IDA]			253
P02747 UniProt NPD GO	C1QC_HUMAN	Complement C1q subcomponent subunit C precursor	0.00	-	cyt	0	Secreted protein	extracellular region [NAS]	120575	1PK6	245
P83301 UniProt NPD GO	CXO_CONVE	Conotoxin	0.00	-	cyt	0	Secreted protein	extracellular region [NAS]			33
P18513 UniProt NPD GO	CXKK2_CONTE	Conotoxin King-Kong 2 precursor (KK-2)	0.00	-	exc	0	Secreted protein				77
Q6PN80 UniProt NPD GO	CX52_CONLE	Conotoxin Lp5.2 precursor	0.00	-	end	0	Secreted protein (By similarity)				68
P58843 UniProt NPD GO	CX6A_CONQU	Conotoxin QcVIA	0.00	-	nuc	0	Secreted protein				25

You are viewing entries 93201 to 93250 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.