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
Q875M2 UniProt NPD GO	AKR1_KLULA	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.02	-	end	7	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				752
Q876L5 UniProt NPD GO	AKR1_SACBA	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.02	-	end	4	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				763
P84276 UniProt NPD GO	PA1C_RANPA	Palustrin-1c	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			27
P84279 UniProt NPD GO	PA2B_RANPA	Palustrin-2b	0.02	-	cyt	0	Secreted protein	extracellular region [IDA]			31
P84280 UniProt NPD GO	PA2C_RANPA	Palustrin-2c	0.02	-	cyt	0	Secreted protein	extracellular region [IDA]			31
P04746 UniProt NPD GO	AMYP_HUMAN	Pancreatic alpha-amylase precursor (EC 3.2.1.1) (PA) (1,4-alpha-D-glucan glucanohydrolase)	0.02	-	pox	0	Secreted protein; extracellular space	extracellular space [TAS]	104650	3CPU	511
P00690 UniProt NPD GO	AMYP_PIG	Pancreatic alpha-amylase precursor (EC 3.2.1.1) (PA) (1,4-alpha-D-glucan glucanohydrolase)	0.02	-	pox	0	Secreted protein; extracellular space			1WO2	511
P00996 UniProt NPD GO	IPK1_BOVIN	Pancreatic secretory trypsin inhibitor precursor	0.02	-	exc	0	Secreted protein				79
P83629 UniProt NPD GO	LIPP_FELCA	Pancreatic triacylglycerol lipase (EC 3.1.1.3) (Pancreatic lipase) (PL) (Fragment)	0.02	-	cyt	0	Secreted protein				25
P83312 UniProt NPD GO	PBPO_PARSC	Parabutoporin	0.02	-	cyt	0	Secreted protein				45
P80079 UniProt NPD GO	PRVA_FELCA	Parvalbumin alpha	0.02	-	cyt	0					109
P32848 UniProt NPD GO	PRVA_MOUSE	Parvalbumin alpha	0.02	-	cyt	0		axon [IDA] cytoplasm [IDA]			109
P02630 UniProt NPD GO	PRVA_RAJCL	Parvalbumin alpha	0.02	-	cyt	0					109
Q04108 UniProt NPD GO	PR04_LYCES	Pathogenesis-related leaf protein 4 precursor (P4)	0.02	-	vac	0					159
P25985 UniProt NPD GO	PR1_PHAVU	Pathogenesis-related protein 1 (PvPR1) (PR2)	0.02	-	cyt	0					155
P33154 UniProt NPD GO	PR1_ARATH	Pathogenesis-related protein 1 precursor (PR-1)	0.02	-	exc	0	Secreted protein; extracellular space; apoplast. Accumulates in the apoplast before secretion				161
P07053 UniProt NPD GO	PR1B_TOBAC	Pathogenesis-related protein 1B precursor (PR-1B)	0.02	-	exc	0	Vacuole. Accumulates in within the vacuoles of specialized cells known as crystal idioblasts				168
Q40374 UniProt NPD GO	PR1_MEDTR	Pathogenesis-related protein PR-1 precursor	0.02	-	exc	1 *					173
Q41359 UniProt NPD GO	PR1_SAMNI	Pathogenesis-related protein PR-1 type precursor	0.02	-	cyt	1 *					167
P83343 UniProt NPD GO	PR4_PRUPE	Pathogenesis-related protein PR-4 (PpAz89) (Fragment)	0.02	-	cyt	0					107
P17872 UniProt NPD GO	PME_ASPTU	Pectinesterase precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.02	-	exc	0					331
Q963C4 UniProt NPD GO	PEN2B_PENVA	Penaeidin-2b precursor (Pen-2b)	0.02	-	end	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				72
Q10735 UniProt NPD GO	PEPB_PIG	Pepsin B precursor (EC 3.4.23.2) (Parapepsin I) (Fragment)	0.02	-	mit	0	Secreted protein				67
Q9Y0X5 UniProt NPD GO	KA1_MESMA	Peptide BmKa1 precursor (BmK2) (Acidic venom peptide Ka1)	0.02	-	exc	0	Secreted protein				57
P0C175 UniProt NPD GO	SCKP2_TITSE	Peptide TsPep2 precursor	0.02	-	vac	0	Secreted protein				68
P10082 UniProt NPD GO	PYY_HUMAN	Peptide YY precursor (PYY) (PYY-I) (Peptide tyrosine tyrosine) [Contains: Peptide YY(3-36) (PYY-II)] ...	0.02	-	exc	1 *	Secreted protein	soluble fraction [TAS]	600781		97
Q9D6Y7 UniProt NPD GO	MSRA_MOUSE	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (PMSR) (P ...	0.02	-	mit	0					233
P69930 UniProt NPD GO	TXAM2_ANTMC	Peptide toxin Am II precursor	0.02	-	exc	0	Secreted protein (By similarity). Found in nematocyst (By similarity)				80
O76537 UniProt NPD GO	PGRP_TRINI	Peptidoglycan recognition protein precursor	0.02	-	cyt	0					182
Q9JLN4 UniProt NPD GO	PGRP_RAT	Peptidoglycan recognition protein precursor (Peptidoglycan recognition protein short) (PGRP-S)	0.02	-	cyt	0	Secreted protein; cytoplasmic granule (By similarity)				183
Q765P4 UniProt NPD GO	PGRP1_HOLDI	Peptidoglycan-recognition protein 1 precursor (Hd-PGRP-1)	0.02	-	cyt	0	Secreted protein				197
Q765P3 UniProt NPD GO	PGRP2_HOLDI	Peptidoglycan-recognition protein 2 precursor (Hd-PGRP-2)	0.02	-	vac	1 *	Secreted protein				187
P34887 UniProt NPD GO	CYPH_ALLCE	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.02	-	cyt	0	Cytoplasm (By similarity)				150
O00845 UniProt NPD GO	PPIA_PARPR	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.02	-	cyt	0					162
Q4WP12 UniProt NPD GO	PPIB_ASPFU	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.02	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				209
P30412 UniProt NPD GO	PPIC_MOUSE	Peptidyl-prolyl cis-trans isomerase C (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin C)	0.02	-	exc	0	Cytoplasm			2RMC	212
P34790 UniProt NPD GO	CP18C_ARATH	Peptidyl-prolyl cis-trans isomerase CYP18-3 (EC 5.2.1.8) (PPIase CYP18-3) (Rotamase cyclophilin-1) ( ...	0.02	-	cyt	0	Cytoplasm (Probable)				172
Q9SKQ0 UniProt NPD GO	CP19B_ARATH	Peptidyl-prolyl cis-trans isomerase CYP19-2 (EC 5.2.1.8) (PPIase CYP19-2) (Rotamase cyclophilin-6) ( ...	0.02	-	cyt	0	Cytoplasm (Probable)				174
Q4HXF6 UniProt NPD GO	PPID_GIBZE	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.02	-	cyt	0	Cytoplasm (By similarity)				372
P35176 UniProt NPD GO	CYPD_YEAST	Peptidyl-prolyl cis-trans isomerase D precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin D)	0.02	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	cytoplasm [IDA] endoplasmic reticulum [IDA]			225
Q9CWW6 UniProt NPD GO	PIN4_MOUSE	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (EC 5.2.1.8) (Rotamase Pin4) (PPIase Pin4)	0.02	-	cyt	0					131
Q7RYY4 UniProt NPD GO	PIN4_NEUCR	Peptidyl-prolyl cis-trans isomerase pin-4 (EC 5.2.1.8) (PPIase pin-4) (Parvulin pin-4)	0.02	-	nuc	0					130
Q4WJM6 UniProt NPD GO	PIN4_ASPFU	Peptidyl-prolyl cis-trans isomerase pin4 (EC 5.2.1.8) (PPIase pin4) (Parvulin pin4)	0.02	-	nuc	0					129
Q4WCR3 UniProt NPD GO	PPIL1_ASPFU	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.02	-	cyt	0					161
Q9D0W5 UniProt NPD GO	PPIL1_MOUSE	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.02	-	cyt	0					166
Q4IPB8 UniProt NPD GO	PPIL3_GIBZE	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.02	-	cyt	0					167
O04287 UniProt NPD GO	FKB12_VICFA	Peptidyl-prolyl isomerase FKBP12 (EC 5.2.1.8) (12 kDa FK506-binding protein) (12 kDa FKBP) (FKBP-12) ...	0.02	-	cyt	0	Cytoplasm (Potential)				112
P80483 UniProt NPD GO	PCP3_AMPCA	Peridinin-chlorophyll a-binding protein 3 (PCP)	0.02	-	cyt	0	Plastid; chloroplast				323
P30535 UniProt NPD GO	BZRP_BOVIN	Peripheral-type benzodiazepine receptor (PBR) (PKBS) (Isoquinoline-binding protein) (IBP)	0.02	-	cyt	5 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				169
P84655 UniProt NPD GO	PVK1_BANRO	Periviscerokinin-1 (Banro-PVK-1)	0.02	-		0	Secreted protein				11

You are viewing entries 84851 to 84900 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.