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
Q923M1 UniProt NPD GO	MSRA_RAT	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (PMSR) (P ...	0.04	-	mit	0					233
P40029 UniProt NPD GO	MSRA_YEAST	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.04	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			184
P84815 UniProt NPD GO	PTYA_RANSV	Peptide tyrosine arginine	0.04	-		0	Secreted protein	extracellular region [IDA]			18
P84004 UniProt NPD GO	PYF_LOLVU	Peptide tyrosine phenylalanine (PYF) (Neuropeptide F-related peptide)	0.04	-		0	Secreted protein				9
Q96LB8 UniProt NPD GO	PGRP4_HUMAN	Peptidoglycan recognition protein I-beta precursor (Peptidoglycan recognition protein intermediate b ...	0.04	-	mit	0	Membrane; peripheral membrane protein (Potential)	intracellular [NAS] membrane [NAS]	608198		373
Q9V4X2 UniProt NPD GO	PGSC2_DROME	Peptidoglycan-recognition protein-SC2 precursor (EC 3.5.1.28)	0.04	-	exc	1 *	Secreted protein (Potential)	extracellular region [ISS]			184
P14088 UniProt NPD GO	PPIA_ECHGR	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.04	-	cyt	0	Cytoplasm				162
Q26565 UniProt NPD GO	PPIA_SCHMA	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.04	-	nuc	0					161
Q7S7Z6 UniProt NPD GO	PPIB_NEUCR	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.04	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				207
Q6C4W6 UniProt NPD GO	PPIB_YARLI	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				228
O94273 UniProt NPD GO	PPIB_SCHPO	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B) (Cyclophilin 4) ...	0.04	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen				201
P24367 UniProt NPD GO	PPIB_CHICK	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (S- ...	0.04	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				207
P24368 UniProt NPD GO	PPIB_RAT	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (S- ...	0.04	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				208
Q9SP02 UniProt NPD GO	CP20A_ARATH	Peptidyl-prolyl cis-trans isomerase CYP20-1 precursor (EC 5.2.1.8) (PPIase CYP20-1) (Rotamase cyclop ...	0.04	-	exc	0	Endoplasmic reticulum (By similarity). Secreted protein (By similarity)				204
Q6BXZ7 UniProt NPD GO	PPID_DEBHA	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.04	-	cyt	0	Cytoplasm (By similarity)				370
P0C1I1 UniProt NPD GO	PPID_RHIOR	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.04	-	cyt	0	Cytoplasm (By similarity)				364
Q9UNP9 UniProt NPD GO	PPIE_HUMAN	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) (PPIase E) (Rotamase E) (Cyclophilin E) (Cyclophi ...	0.04	-	cyt	0	Nucleus	nucleus [IDA]	602435	2CQB	301
P0C1I3 UniProt NPD GO	PPIH_RHIOR	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.04	-	cyt	0	Nucleus (By similarity)				178
Q5KKX7 UniProt NPD GO	PPIL1_CRYNE	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.04	-	cyt	0					174
Q4I1Y1 UniProt NPD GO	PPIL1_GIBZE	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.04	-	cyt	0					162
Q7SF72 UniProt NPD GO	PPIL1_NEUCR	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.04	-	cyt	0					153
Q5BAH7 UniProt NPD GO	PPIL3_EMENI	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.04	-	cyt	0					211
Q04536 UniProt NPD GO	PER_DROSA	Period circadian protein (Fragment)	0.04	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				66
P84663 UniProt NPD GO	PVK3_DERVE	Periviscerokinin-3 (Derve-PVK-3)	0.04	-		0	Secreted protein				11
Q9SS67 UniProt NPD GO	PER28_ARATH	Peroxidase 28 precursor (EC 1.11.1.7) (Atperox P28) (ATP39)	0.04	-	vac	1 *	Secreted protein (By similarity)				321
O23609 UniProt NPD GO	PER41_ARATH	Peroxidase 41 precursor (EC 1.11.1.7) (Atperox P41)	0.04	-	end	0	Secreted protein (By similarity)				326
Q43872 UniProt NPD GO	PER64_ARATH	Peroxidase 64 precursor (EC 1.11.1.7) (Atperox P64) (PRXR4) (ATP17a)	0.04	-	nuc	0	Secreted protein (By similarity)				317
Q9V3P0 UniProt NPD GO	PRDX1_DROME	Peroxiredoxin 1 (EC 1.11.1.15) (Thioredoxin peroxidase) (Cytosolic thioredoxin peroxidase) (DmTPx-1) ...	0.04	-	cyt	0	Cytoplasm	cytosol [IDA]			194
Q9WUR2 UniProt NPD GO	PECI_MOUSE	Peroxisomal 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delta(3),delta(2) ...	0.04	-	mit	0	Peroxisome; peroxisomal matrix				358
P0C024 UniProt NPD GO	NUDT7_HUMAN	Peroxisomal coenzyme A diphosphatase NUDT7 (EC 3.6.1.-) (Nucleoside diphosphate-linked moiety X moti ...	0.04	-	nuc	0	Peroxisome (By similarity)		609231		238
P38137 UniProt NPD GO	FAT2_YEAST	Peroxisomal-coenzyme A synthetase (EC 6.-.-.-)	0.04	-	pox	0	Peroxisome. Peroxisomal matrix and at the peroxisomal peripheral membrane	cytoplasm [IDA] peroxisomal matrix [IDA] peroxisomal membrane [IDA]			543
P33751 UniProt NPD GO	PAD1_YEAST	Phenylacrylic acid decarboxylase (EC 4.1.1.-) (PAD)	0.04	-	mit	0	Cytoplasm	mitochondrion [IDA]			242
Q40910 UniProt NPD GO	PAL4_POPKI	Phenylalanine ammonia-lyase G4 (EC 4.3.1.5) (Fragment)	0.04	-	nuc	0	Cytoplasm (Probable)				571
P19143 UniProt NPD GO	PAL3_PHAVU	Phenylalanine ammonia-lyase class 3 (EC 4.3.1.5) (Phenylalanine ammonia-lyase class III)	0.04	-	nuc	0	Cytoplasm (Probable)				710
P11086 UniProt NPD GO	PNMT_HUMAN	Phenylethanolamine N-methyltransferase (EC 2.1.1.28) (PNMTase) (Noradrenaline N-methyltransferase)	0.04	-	cyt	0			171190	2AN5	282
O61703 UniProt NPD GO	MPCP_CHOFU	Phosphate carrier protein, mitochondrial precursor (Phosphate transport protein) (PTP)	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				349
Q91XU8 UniProt NPD GO	CDS2_RAT	Phosphatidate cytidylyltransferase 2 (EC 2.7.7.41) (CDP-diglyceride synthetase 2) (CDP-diglyceride p ...	0.04	-	end	8	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				443
O35573 UniProt NPD GO	LCAT_ELIQU	Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) (Lecithin-cholesterol acyltransferase) (Pho ...	0.04	-	cyt	0					299
Q8NHU3 UniProt NPD GO	SMS2_HUMAN	Phosphatidylcholine:ceramide cholinephosphotransferase 2 (EC 2.7.-.-) (Sphingomyelin synthase 2)	0.04	-	end	6	Cell membrane; multi-pass membrane protein. Golgi apparatus; Golgi membrane; multi-pass membrane pro ...	Golgi apparatus [IDA] integral to Golgi membrane [IDA] integral to plasma membrane [IDA]			365
P31044 UniProt NPD GO	PEBP1_RAT	Phosphatidylethanolamine-binding protein 1 (PEBP-1) (HCNPpp) (23 kDa morphine-binding protein) (P23K ...	0.04	+	cyt	0	Cytoplasm. Membrane; peripheral membrane protein				186
P13696 UniProt NPD GO	PEBP1_BOVIN	Phosphatidylethanolamine-binding protein 1 (PEBP-1) (HCNPpp) (Basic cytosolic 21 kDa protein) [Conta ...	0.04	+	cyt	0	Cytoplasm			1B7A	186
P48737 UniProt NPD GO	PEBP1_MACFA	Phosphatidylethanolamine-binding protein 1 (PEBP-1) (HCNPpp) [Contains: Hippocampal cholinergic neur ...	0.04	+	cyt	0	Cytoplasm				186
Q5R4R0 UniProt NPD GO	PEBP1_PONPY	Phosphatidylethanolamine-binding protein 1 (PEBP-1) (HCNPpp) [Contains: Hippocampal cholinergic neur ...	0.04	+	cyt	0	Cytoplasm (By similarity)				186
P30086 UniProt NPD GO	PEBP1_HUMAN	Phosphatidylethanolamine-binding protein 1 (PEBP-1) (Prostatic-binding protein) (HCNPpp) (Neuropolyp ...	0.04	+	cyt	0	Cytoplasm (By similarity)		604591	1BEH	186
Q6CHU5 UniProt NPD GO	NPC2_YARLI	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.04	-	vac	0					189
P10963 UniProt NPD GO	PPCK_YEAST	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.04	-	cyt	0		cytosol [IDA]			549
P35558 UniProt NPD GO	PPCKC_HUMAN	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) ( ...	0.04	-	nuc	0	Cytoplasm		261680	1NHX	622
Q5R5J1 UniProt NPD GO	PPCKC_PONPY	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) ( ...	0.04	-	nuc	0	Cytoplasm (By similarity)				622
Q9SM60 UniProt NPD GO	PGMC_PEA	Phosphoglucomutase, cytoplasmic (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.04	-	cyt	0	Cytoplasm (By similarity)				582
P50311 UniProt NPD GO	PGK_OPISI	Phosphoglycerate kinase (EC 2.7.2.3)	0.04	-	cyt	0	Cytoplasm (Potential)				415

You are viewing entries 77851 to 77900 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.