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
Q70XU7 UniProt NPD GO	RR12_AMBTC	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				123
P62126 UniProt NPD GO	RR12_ARATH	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				122
Q8RUK6 UniProt NPD GO	RR12_ATRBE	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				123
Q7Y677 UniProt NPD GO	RR12_CALFE	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				123
Q9TLV6 UniProt NPD GO	RR12_CYACA	Chloroplast 30S ribosomal protein S12	0.22	-	nuc	0	Plastid; chloroplast				124
P62127 UniProt NPD GO	RR12_NICPL	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				122
Q6EW28 UniProt NPD GO	RR12_NYMAL	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				123
Q68S28 UniProt NPD GO	RR12_PANGI	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				123
P62128 UniProt NPD GO	RR12_SPIOL	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				122
P62129 UniProt NPD GO	RR12_TOBAC	Chloroplast 30S ribosomal protein S12	0.22	-	mit	0	Plastid; chloroplast				122
P56806 UniProt NPD GO	RR16_ARATH	Chloroplast 30S ribosomal protein S16	0.22	-	mit	0	Plastid; chloroplast				79
Q85G24 UniProt NPD GO	RR16_CYAME	Chloroplast 30S ribosomal protein S16	0.22	-	mit	0	Plastid; chloroplast				75
P15762 UniProt NPD GO	RR19_SINAL	Chloroplast 30S ribosomal protein S19 (Fragment)	0.22	-	nuc	0	Plastid; chloroplast				48
Q9TL03 UniProt NPD GO	RR2_NEPOL	Chloroplast 30S ribosomal protein S2	0.22	-	cyt	0	Plastid; chloroplast				272
P49494 UniProt NPD GO	RR6_ODOSI	Chloroplast 30S ribosomal protein S6	0.22	-	nuc	0	Plastid; chloroplast				96
Q6B8W6 UniProt NPD GO	RR8_GRATL	Chloroplast 30S ribosomal protein S8	0.22	-	cyt	0	Plastid; chloroplast				132
Q2PMQ0 UniProt NPD GO	RR8_SOYBN	Chloroplast 30S ribosomal protein S8	0.22	-	cyt	0	Plastid; chloroplast				134
P56368 UniProt NPD GO	RK23_CHLVU	Chloroplast 50S ribosomal protein L23	0.22	-	nuc	0	Plastid; chloroplast				86
Q6B8W1 UniProt NPD GO	RK29_GRATL	Chloroplast 50S ribosomal protein L29	0.22	-	nuc	0	Plastid; chloroplast				66
Q95H56 UniProt NPD GO	RK33_WHEAT	Chloroplast 50S ribosomal protein L33	0.22	-	nuc	0	Plastid; chloroplast				66
P56362 UniProt NPD GO	RK5_CHLVU	Chloroplast 50S ribosomal protein L5	0.22	-	cyt	0	Plastid; chloroplast				180
Q8N6G5 UniProt NPD GO	CGAT2_HUMAN	Chondroitin beta-1,4-N-acetylgalactosaminyltransferase 2 (EC 2.4.1.174) (GalNAcT-2) (beta4GalNAcT-2) ...	0.22	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)	integral to Golgi membrane [NAS]			542
Q76LD0 UniProt NPD GO	CRDL1_RAT	Chordin-like protein 1 precursor (Kohjirin)	0.22	-	exc	0	Secreted protein (Potential)	extracellular region [TAS]			447
P09321 UniProt NPD GO	CSH2_RAT	Chorionic somatomammotropin hormone 2 precursor (Placental lactogen II) (PL-II) (RPLII)	0.22	-	vac	0	Secreted protein	extracellular space [IDA]			221
P42738 UniProt NPD GO	CHMU_ARATH	Chorismate mutase, chloroplast precursor (EC 5.4.99.5) (CM-1)	0.22	-	nuc	0	Plastid; chloroplast				334
Q75AH9 UniProt NPD GO	EAF3_ASHGO	Chromatin modification-related protein EAF3	0.22	-	cyt	0	Nucleus (By similarity)				310
P21842 UniProt NPD GO	MCPT1_CANFA	Chymase precursor (EC 3.4.21.39) (Mast cell protease I)	0.22	-	end	0					249
O19045 UniProt NPD GO	FA10_RABIT	Coagulation factor X precursor (EC 3.4.21.6) (Stuart factor) [Contains: Factor X light chain; Factor ...	0.22	-	nuc	1 *					490
Q91Y47 UniProt NPD GO	FA11_MOUSE	Coagulation factor XI precursor (EC 3.4.21.27) (Plasma thromboplastin antecedent) (PTA) (FXI) [Conta ...	0.22	-	cyt	0	Secreted protein				624
O08619 UniProt NPD GO	F13A_RAT	Coagulation factor XIII A chain precursor (EC 2.3.2.13) (Coagulation factor XIIIa) (Protein-glutamin ...	0.22	-	cyt	0	Cytoplasm (By similarity). Secreted protein (By similarity). Cytoplasmic in most tissues, but also s ...				731
Q16568 UniProt NPD GO	CART_HUMAN	Cocaine- and amphetamine-regulated transcript protein precursor [Contains: CART(1-39); CART(42-89)]	0.22	-	exc	0	Secreted protein (Potential)	extracellular space [TAS]	602606	1HY9	116
Q9D9B0 UniProt NPD GO	CCD70_MOUSE	Coiled-coil domain-containing protein 70 precursor	0.22	-	mit	0	Secreted protein (Potential)				223
P02459 UniProt NPD GO	CO2A1_BOVIN	Collagen alpha-1(II) chain precursor (Fragments)	0.22	-	nuc	0					747
Q02388 UniProt NPD GO	CO7A1_HUMAN	Collagen alpha-1(VII) chain precursor (Long-chain collagen) (LC collagen)	0.22	-	nuc	0		basement membrane [TAS] collagen type VII [TAS]	607600		2944
Q9P218 UniProt NPD GO	COKA1_HUMAN	Collagen alpha-1(XX) chain precursor	0.22	-	mit	0	Secreted protein; extracellular space (Probable)				1329
P02465 UniProt NPD GO	CO1A2_BOVIN	Collagen alpha-2(I) chain precursor	0.22	-	exc	0					1364
P02467 UniProt NPD GO	CO1A2_CHICK	Collagen alpha-2(I) chain precursor (Fragments)	0.22	-	exc	0					1362
P08122 UniProt NPD GO	CO4A2_MOUSE	Collagen alpha-2(IV) chain precursor	0.22	-	mit	1 *		collagen type IV [IDA]			1707
Q14050 UniProt NPD GO	CO9A3_HUMAN	Collagen alpha-3(IX) chain precursor	0.22	-	exc	0		collagen type IX [TAS]	600969		684
Q9ESG4 UniProt NPD GO	TMM27_MOUSE	Collectrin precursor (Transmembrane protein 27)	0.22	-	end	1	Membrane; single-pass type I membrane protein (Potential)				222
P00736 UniProt NPD GO	C1R_HUMAN	Complement C1r subcomponent precursor (EC 3.4.21.41) (Complement component 1, r subcomponent) [Conta ...	0.22	-	mit	0		extracellular region [NAS]	216950	1MD8	705
Q5R1W3 UniProt NPD GO	C1R_PANTR	Complement C1r subcomponent precursor (EC 3.4.21.41) (Complement component 1, r subcomponent) [Conta ...	0.22	-	mit	0					705
Q03710 UniProt NPD GO	CFAB_PIG	Complement factor B (EC 3.4.21.47) (C3/C5 convertase) (Properdin factor B) (Fragment)	0.22	-	nuc	0	Secreted protein				151
Q02985 UniProt NPD GO	FHR3_HUMAN	Complement factor H-related protein 3 precursor (FHR-3) (H factor-like protein 3) (DOWN16)	0.22	-	exc	0	Secreted protein	extracellular space [TAS]	605336		330
P97846 UniProt NPD GO	CNTP1_RAT	Contactin-associated protein 1 precursor (Caspr) (Caspr1) (Neurexin 4) (Neurexin IV) (p190) (Paranod ...	0.22	-	end	1	Membrane; single-pass type I membrane protein (Potential)	axon [IDA] integral to membrane [IDA]			1381
Q86YQ8 UniProt NPD GO	CPNE8_HUMAN	Copine-8 (Copine VIII)	0.22	-	cyt	0					564
Q9DC53 UniProt NPD GO	CPNE8_MOUSE	Copine-8 (Copine VIII)	0.22	-	cyt	0					564
Q29437 UniProt NPD GO	AOCX_BOVIN	Copper amine oxidase, liver isozyme precursor (EC 1.4.3.6) (Amine oxidase [copper-containing]) (Seru ...	0.22	-	nuc	0	Secreted protein; extracellular space			1TU5	762
Q5TM45 UniProt NPD GO	CDSN_MACMU	Corneodesmosin precursor	0.22	-	nuc	0	Secreted protein. Found in corneodesmosomes, the intercellular structures that are involved in desqu ...				534
Q15517 UniProt NPD GO	CDSN_HUMAN	Corneodesmosin precursor (S protein)	0.22	-	exc	1 *	Secreted protein. Found in corneodesmosomes, the intercellular structures that are involved in desqu ...	cornified envelope [IDA] desmosome [NAS]	602593		529

You are viewing entries 48251 to 48300 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.