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
P35182 UniProt NPD GO	PP2C1_YEAST	Protein phosphatase 2C homolog 1 (EC 3.1.3.16) (PP2C-1)	0.04	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			281
P56330 UniProt NPD GO	SUI1_MAIZE	Protein translation factor SUI1 homolog (Protein GOS2)	0.04	-	cyt	0					115
P33278 UniProt NPD GO	SUI1_ORYSA	Protein translation factor SUI1 homolog (Protein GOS2) (Translational initiation factor 1) (Protein ...	0.04	-	cyt	0					115
Q04491 UniProt NPD GO	SEC13_YEAST	Protein transport protein SEC13	0.04	-	cyt	0	Endoplasmic reticulum. Nucleus; nuclear envelope; nuclear pore complex. COPII	COPII vesicle coat [IDA] cytoplasm [IDA] extrinsic to membrane [IDA] nuclear pore [IGI]			297
Q7Z1B8 UniProt NPD GO	S61G1_GRYOR	Protein transport protein SEC61 subunit gamma	0.04	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				68
P60467 UniProt NPD GO	SC61B_CANFA	Protein transport protein Sec61 subunit beta	0.04	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				95
P60468 UniProt NPD GO	SC61B_HUMAN	Protein transport protein Sec61 subunit beta	0.04	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein		609214		95
Q9CQS8 UniProt NPD GO	SC61B_MOUSE	Protein transport protein Sec61 subunit beta	0.04	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				95
Q5RB31 UniProt NPD GO	SC61B_PONPY	Protein transport protein Sec61 subunit beta	0.04	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				95
Q9USJ2 UniProt NPD GO	GOT1_SCHPO	Protein transport protein got1 (Golgi transport protein 1)	0.04	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				129
P54356 UniProt NPD GO	TSG_DROME	Protein twisted gastrulation precursor	0.04	-	cyt	0	Secreted protein	extracellular region [IPI]			249
P10379 UniProt NPD GO	UZIP_DROME	Protein unzipped precursor (Protein zipper)	0.04	-	exc	1 *	Membrane; single-pass type I membrane protein				488
Q9BI23 UniProt NPD GO	YELL_DROER	Protein yellow precursor	0.04	-	exc	0	Secreted protein				541
Q9BI18 UniProt NPD GO	YELL_DROPS	Protein yellow precursor	0.04	-	mit	1 *	Secreted protein				560
P45845 UniProt NPD GO	LYOX_PIG	Protein-lysine 6-oxidase (EC 1.4.3.13) (Lysyl oxidase) (Fragment)	0.04	-	cyt	0	Secreted protein; extracellular space				36
P0C089 UniProt NPD GO	PTPM1_RAT	Protein-tyrosine phosphatase mitochondrial 1, mitochondrial precursor (EC 3.1.3.48) (EC 3.1.3.16)	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Associated with the inner membrane (By ...				193
P83578 UniProt NPD GO	IKP1_PHYSA	Proteinase inhibitor PSKP-1	0.04	-	nuc	0	Secreted protein	extracellular region [IDA]			58
P01079 UniProt NPD GO	IP21_SOLTU	Proteinase inhibitor PTI	0.04	-	nuc	0	Secreted protein				51
Q43710 UniProt NPD GO	IP22_LYCES	Proteinase inhibitor type-2 TR8 precursor (Proteinase inhibitor type II TR8)	0.04	-	exc	0					223
Q58D85 UniProt NPD GO	PAR3_BOVIN	Proteinase-activated receptor 3 precursor (PAR-3) (Thrombin receptor-like 2) (Coagulation factor II ...	0.04	-	end	7	Membrane; multi-pass membrane protein				377
Q920E1 UniProt NPD GO	PAR3_RAT	Proteinase-activated receptor 3 precursor (PAR-3) (Thrombin receptor-like 2) (Coagulation factor II ...	0.04	-	end	7	Membrane; multi-pass membrane protein				368
O88634 UniProt NPD GO	PAR4_MOUSE	Proteinase-activated receptor 4 precursor (PAR-4) (Thrombin receptor-like 3) (Coagulation factor II ...	0.04	-	end	7	Membrane; multi-pass membrane protein				396
Q95MN6 UniProt NPD GO	PLP2_RABIT	Proteolipid protein 2	0.04	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				152
P15904 UniProt NPD GO	POR_AVESA	Protochlorophyllide reductase (EC 1.3.1.33) (PCR) (NADPH-protochlorophyllide oxidoreductase) (POR) ( ...	0.04	-	cyt	0	Plastid; chloroplast				313
Q39617 UniProt NPD GO	POR_CHLRE	Protochlorophyllide reductase, chloroplast precursor (EC 1.3.1.33) (PCR) (NADPH-protochlorophyllide ...	0.04	-	mit	0	Plastid; chloroplast				397
P29263 UniProt NPD GO	PH1_PRUSE	Prunasin beta-glucosidase 1 (EC 3.2.1.118) (Prunasin beta-glucosidase I) (Prunasin hydrolase isozyme ...	0.04	-		0					14
P61457 UniProt NPD GO	PHS_HUMAN	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.04	-	cyt	0	Cytoplasm. Nucleus. Cytoplasmic and/or nuclear		264070		103
P61459 UniProt NPD GO	PHS_RAT	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.04	-	cyt	0	Cytoplasm. Nucleus. Cytoplasmic and/or nuclear			1F93	103
P06908 UniProt NPD GO	SFTPA_CANFA	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.04	-	exc	0	Secreted protein; extracellular space				248
Q95L88 UniProt NPD GO	SFTPA_HORSE	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.04	-	exc	0	Secreted protein; extracellular space (By similarity)				248
P15782 UniProt NPD GO	PSPB_PIG	Pulmonary surfactant-associated protein B (SP-B) (8 kDa protein) (Pulmonary surfactant-associated pr ...	0.04	-	cyt	0	Secreted protein; extracellular space				79
P80685 UniProt NPD GO	CUG1A_TENMO	Pupal cuticle protein G1A (TM-G1A) (TM-PCP G1A)	0.04	-	mit	0					211
P82868 UniProt NPD GO	SB60_MAIZE	Putative 60 kDa spermidine-binding protein (Fragment)	0.04	-		0	Microsome; microsomal membrane	microsome [NAS]			20
O35127 UniProt NPD GO	C10_MOUSE	Putative C10 protein (B-cell receptor-associated protein 37)	0.04	-	cyt	0					126
P34480 UniProt NPD GO	NAGA_CAEEL	Putative N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (GlcNAc 6-P deacetylase)	0.04	-	cyt	0					418
Q09707 UniProt NPD GO	YA39_SCHPO	Putative acetyltransferase C18B11.09c (EC 2.3.1.-)	0.04	-	mit	2					207
P40892 UniProt NPD GO	YJV8_YEAST	Putative acetyltransferase YJL218W (EC 2.3.1.-)	0.04	-	cyt	0					196
P84734 UniProt NPD GO	PS18_PINST	Putative acid phosphatase PS18 (Fragment)	0.04	-		0					9
Q10087 UniProt NPD GO	YAO8_SCHPO	Putative amino-acid permease C11D3.08c	0.04	-	end	12	Membrane; multi-pass membrane protein (Potential)				550
O74537 UniProt NPD GO	YCQ4_SCHPO	Putative amino-acid permease C74.04	0.04	-	end	12	Membrane; multi-pass membrane protein (Potential)				557
P34479 UniProt NPD GO	YMJ2_CAEEL	Putative amino-acid permease F59B2.2	0.04	-	end	10	Membrane; multi-pass membrane protein (Potential)				460
Q27245 UniProt NPD GO	YH24_CAEEL	Putative aminopeptidase W07G4.4 in chromosome V (EC 3.4.11.-)	0.04	-	mit	0					522
Q09369 UniProt NPD GO	AQP10_CAEEL	Putative aquaporin-10	0.04	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				280
Q9LP07 UniProt NPD GO	ARFW_ARATH	Putative auxin response factor 23	0.04	-	cyt	0	Nucleus				222
Q9M1R4 UniProt NPD GO	IAA30_ARATH	Putative auxin-responsive protein IAA30 (Putative indoleacetic acid-induced protein 30)	0.04	-	mit	0	Nucleus (By similarity)				172
Q9M203 UniProt NPD GO	EXPB5_ARATH	Putative beta-expansin 5 precursor (AtEXPB5) (At-EXPB5) (Ath-ExpBeta-1.3)	0.04	-	nuc	0	Cell wall; peripheral membrane protein				264
Q05957 UniProt NPD GO	CPPM_DIACA	Putative carboxyvinyl-carboxyphosphonate phosphorylmutase (EC 2.7.8.23) (Carboxyphosphonoenolpyruvat ...	0.04	-	cyt	0				1ZLP	318
P34465 UniProt NPD GO	CY561_CAEEL	Putative cytochrome b561 (Cytochrome b-561)	0.04	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				266
P93280 UniProt NPD GO	CCMB_ARATH	Putative cytochrome c biogenesis ccmB-like mitochondrial protein	0.04	-	end	5 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				206
P38453 UniProt NPD GO	CCMC_MARPO	Putative cytochrome c biosynthesis ccmC-like mitochondrial protein	0.04	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				228

You are viewing entries 78201 to 78250 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.