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
Q9TLV1 UniProt NPD GO	RR11_CYACA	Chloroplast 30S ribosomal protein S11	0.38	-	nuc	0	Plastid; chloroplast				129
Q6B8X3 UniProt NPD GO	RR11_GRATL	Chloroplast 30S ribosomal protein S11	0.38	-	nuc	0	Plastid; chloroplast				129
Q9TL38 UniProt NPD GO	RR14_NEPOL	Chloroplast 30S ribosomal protein S14	0.38	-	nuc	0	Plastid; chloroplast				100
P16631 UniProt NPD GO	RR3_GRATE	Chloroplast 30S ribosomal protein S3	0.38	-	mit	0	Plastid; chloroplast				209
Q32RN6 UniProt NPD GO	RR3_ZYGCR	Chloroplast 30S ribosomal protein S3	0.38	-	nuc	0	Plastid; chloroplast				236
Q9M4C3 UniProt NPD GO	RR4_PLARP	Chloroplast 30S ribosomal protein S4	0.38	-	mit	0	Plastid; chloroplast				202
P51219 UniProt NPD GO	RR4_PORPU	Chloroplast 30S ribosomal protein S4	0.38	-	nuc	0	Plastid; chloroplast				201
Q9TM55 UniProt NPD GO	RR7_BETVU	Chloroplast 30S ribosomal protein S7	0.38	-	nuc	0	Plastid; chloroplast				155
P48267 UniProt NPD GO	RR7_CHLRE	Chloroplast 30S ribosomal protein S7	0.38	-	mit	0	Plastid; chloroplast				168
Q6EM77 UniProt NPD GO	RR7_PHYAM	Chloroplast 30S ribosomal protein S7	0.38	-	nuc	0	Plastid; chloroplast				155
Q589A4 UniProt NPD GO	RR7_SILLA	Chloroplast 30S ribosomal protein S7	0.38	-	nuc	0	Plastid; chloroplast				155
Q9MUU6 UniProt NPD GO	RR8_MESVI	Chloroplast 30S ribosomal protein S8	0.38	+	nuc	0	Plastid; chloroplast				133
P56358 UniProt NPD GO	RR9_CHLVU	Chloroplast 30S ribosomal protein S9	0.38	+	nuc	0	Plastid; chloroplast				137
P56793 UniProt NPD GO	RK16_ARATH	Chloroplast 50S ribosomal protein L16	0.38	-	mit	0	Plastid; chloroplast				135
Q6END6 UniProt NPD GO	RK16_ORYNI	Chloroplast 50S ribosomal protein L16	0.38	-	mit	0	Plastid; chloroplast				136
P17353 UniProt NPD GO	RK16_SPIOL	Chloroplast 50S ribosomal protein L16 (Ribosomal protein CS-L24)	0.38	-	mit	0	Plastid; chloroplast				135
Q32RV5 UniProt NPD GO	RK22_STAPU	Chloroplast 50S ribosomal protein L22	0.38	-	nuc	0	Plastid; chloroplast				132
Q9MSA0 UniProt NPD GO	RK28_GALSU	Chloroplast 50S ribosomal protein L28	0.38	-	mit	0	Plastid; chloroplast				68
Q9BBP5 UniProt NPD GO	RK32_LOTJA	Chloroplast 50S ribosomal protein L32	0.38	-	mit	0	Plastid; chloroplast				50
P28804 UniProt NPD GO	RK32_SPIOL	Chloroplast 50S ribosomal protein L32	0.38	-	nuc	0	Plastid; chloroplast				56
P60246 UniProt NPD GO	RK36_AMBTC	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
P62117 UniProt NPD GO	RK36_ARATH	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
P62119 UniProt NPD GO	RK36_ATRBE	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
Q7HKX4 UniProt NPD GO	RK36_CALFE	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
Q9TL26 UniProt NPD GO	RK36_NEPOL	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
Q68RX3 UniProt NPD GO	RK36_PANGI	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
P51296 UniProt NPD GO	RK36_PORPU	Chloroplast 50S ribosomal protein L36	0.38	-	nuc	0	Plastid; chloroplast				37
Q7ICQ6 UniProt NPD GO	RK36_SOYBN	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
P12230 UniProt NPD GO	RK36_SPIOL	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
P62118 UniProt NPD GO	RK36_TOBAC	Chloroplast 50S ribosomal protein L36	0.38	-	mit	0	Plastid; chloroplast				37
Q14406 UniProt NPD GO	CSHL_HUMAN	Chorionic somatomammotropin hormone-like 1 precursor (Chorionic somatomammotropin-like) (Lactogen-li ...	0.38	-	exc	0	Secreted protein		603515		199
O02607 UniProt NPD GO	AROC_TOXGO	Chorismate synthase (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phospholyase)	0.38	-	nuc	0					536
Q8VDS3 UniProt NPD GO	CBX7_MOUSE	Chromobox protein homolog 7	0.38	-	cyt	0	Nucleus				158
P60889 UniProt NPD GO	CBX7_RAT	Chromobox protein homolog 7	0.38	-	cyt	0	Nucleus (By similarity)				158
Q10290 UniProt NPD GO	MAL2_SCHPO	Chromosome segregation protein mal2	0.38	-	nuc	0	Nucleus. Centromeric	inner kinetochore of condensed chromosome [TAS]			303
P30380 UniProt NPD GO	1B02_GORGO	Class I histocompatibility antigen, GOGO-B0102 alpha chain precursor	0.38	-	end	1	Membrane; single-pass type I membrane protein				362
O14579 UniProt NPD GO	COPE_HUMAN	Coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.38	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [ISS]	606942		307
P01025 UniProt NPD GO	CO3_PIG	Complement C3a anaphylatoxin	0.38	-	nuc	0					77
P49457 UniProt NPD GO	DAF_PONPY	Complement decay-accelerating factor precursor (CD55 antigen) (Fragment)	0.38	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				340
Q8I6U3 UniProt NPD GO	CPLX_HIRME	Complexin-1	0.38	-	exc	0	Membrane; lipid-anchor (Potential)				144
O60032 UniProt NPD GO	HYMA_EMENI	Conidiophore development protein hymA	0.38	-	mit	0	Cytoplasm				384
Q8R1U1 UniProt NPD GO	COG4_MOUSE	Conserved oligomeric Golgi complex component 4	0.38	-	cyt	0	Golgi apparatus (By similarity)				785
P68500 UniProt NPD GO	CNTN5_MOUSE	Contactin-5 precursor (Neural recognition molecule NB-2)	0.38	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1098
Q5RAE1 UniProt NPD GO	CPNE3_PONPY	Copine-3 (Copine III)	0.38	-	mit	0					537
O04197 UniProt NPD GO	COI1_ARATH	Coronatine-insensitive protein 1 (F-box/LRR-repeat protein 2) (AtFBL2) (COI-1) (AtCOI1)	0.38	-	cyt	0					592
P57737 UniProt NPD GO	CORO7_HUMAN	Coronin-7 (70 kDa WD repeat tumor rejection antigen homolog)	0.38	-	mit	0	Cytoplasm; cytosol (By similarity). Predominantly. Membrane (By similarity). Also found in membrane ...	Golgi apparatus [ISS] integral to membrane of membrane fraction [ISS] soluble fraction [ISS]			925
Q8WMV3 UniProt NPD GO	CXAR_BOVIN	Coxsackievirus and adenovirus receptor homolog precursor (Coxsackie virus and adenovirus receptor) ( ...	0.38	-	exc	1	Cell membrane; cell-cell junction; single-pass type I membrane protein (By similarity). Localized at ...				365
P33525 UniProt NPD GO	CRU3_BRANA	Cruciferin CRU1 precursor (11S globulin) (12S storage protein) [Contains: Cruciferin CRU1 alpha chai ...	0.38	-	nuc	0					509
Q5IJ48 UniProt NPD GO	CRUM2_HUMAN	Crumbs homolog 2 precursor (Crumbs-like protein 2)	0.38	-	end	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein		609720		1285
Q26377 UniProt NPD GO	CORZ_DROME	Crz precursor [Contains: Corazonin; Corazonin-precursor-related peptide (CPRP)]	0.38	-	nuc	0	Secreted protein	extracellular region [ISS]			154

You are viewing entries 33301 to 33350 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.