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
P62407 UniProt NPD GO	YELL_DROSI	Protein yellow precursor	0.06	-	exc	0	Secreted protein				541
Q9BI17 UniProt NPD GO	YELL_DROYA	Protein yellow precursor	0.06	-	exc	0	Secreted protein				541
Q03199 UniProt NPD GO	IPIB_TOBAC	Proteinase inhibitor I-B precursor (PI-IB) (Inhibitor of microbial serine proteinases major isoform) ...	0.06	-	exc	0	Secreted protein (Potential)				107
Q920E0 UniProt NPD GO	PAR4_RAT	Proteinase-activated receptor 4 precursor (PAR-4) (Thrombin receptor-like 3) (Coagulation factor II ...	0.06	-	end	7	Membrane; multi-pass membrane protein				395
Q6Y1E2 UniProt NPD GO	PLP2_BOVIN	Proteolipid protein 2	0.06	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				152
Q6P742 UniProt NPD GO	PLP2_RAT	Proteolipid protein 2	0.06	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				151
P26794 UniProt NPD GO	PIM1_RAT	Proto-oncogene serine/threonine-protein kinase Pim-1 (EC 2.7.11.1)	0.06	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS]			313
Q9W7J5 UniProt NPD GO	NXLP_PSETE	Pseudonajatoxin b homolog precursor (Pt-bp)	0.06	-	nuc	0	Secreted protein				103
Q5R7K1 UniProt NPD GO	PHS2_PONPY	Pterin-4-alpha-carbinolamine dehydratase 2 (EC 4.2.1.96) (PHS 2) (4-alpha-hydroxy-tetrahydropterin d ...	0.06	-	nuc	0					103
Q9CZL5 UniProt NPD GO	PHS2_MOUSE	Pterin-4-alpha-carbinolamine dehydratase 2 (EC 4.2.1.96) (PHS 2) (4-alpha-hydroxy-tetrahydropterin d ...	0.06	-	cyt	0		nucleus [IPI]		1RU0	103
P12842 UniProt NPD GO	SFTPA_RABIT	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.06	-	vac	0	Secreted protein; extracellular space				247
P27780 UniProt NPD GO	CUP8_DROME	Pupal cuticle protein Edg-84A precursor	0.06	-	exc	0					188
Q85G45 UniProt NPD GO	RPOZ_CYAME	Putative DNA-directed RNA polymerase omega chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase ...	0.06	-	nuc	0	Plastid; chloroplast				49
Q10909 UniProt NPD GO	YS95_CAEEL	Putative G-protein coupled receptor B0244.5	0.06	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				300
Q84MC0 UniProt NPD GO	UGPI4_ARATH	Putative GPI-anchored protein At3g06035 precursor	0.06	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				200
Q5FW48 UniProt NPD GO	ASPD_XENTR	Putative L-aspartate dehydrogenase (EC 1.4.1.21)	0.06	-	cyt	0					284
Q9ZUP0 UniProt NPD GO	LBD8_ARATH	Putative LOB domain-containing protein 8	0.06	-	nuc	0					120
Q09671 UniProt NPD GO	OYEB_SCHPO	Putative NADPH dehydrogenase C5H10.10 (EC 1.6.99.1) (Old yellow enzyme homolog)	0.06	-	cyt	0					392
P91580 UniProt NPD GO	RAB33_CIOIN	Putative Ras-related protein Rab-33	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				218
Q9V813 UniProt NPD GO	MTAP_DROME	Putative S-methyl-5-thioadenosine phosphorylase (EC 2.4.2.28) (5'-methylthioadenosine phosphorylase) ...	0.06	-	cyt	0					289
P59531 UniProt NPD GO	T2R12_HUMAN	Putative Taste receptor type 2 member 12 (T2R12) (Taste receptor type 2 member 26) (T2R26)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				264
Q9P5N4 UniProt NPD GO	YH81_SCHPO	Putative amino-acid permease C359.01	0.06	-	end	12	Membrane; multi-pass membrane protein (Potential)				581
Q9URZ4 UniProt NPD GO	YI0B_SCHPO	Putative amino-acid permease C869.11	0.06	-	end	11	Membrane; multi-pass membrane protein (Potential)				580
P54145 UniProt NPD GO	AMT1_CAEEL	Putative ammonium transporter 1	0.06	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				534
P22702 UniProt NPD GO	AR2LP_NEUCR	Putative arg-2 leader peptide	0.06	-	nuc	0					24
Q08361 UniProt NPD GO	AAD15_YEAST	Putative aryl-alcohol dehydrogenase AAD15 (EC 1.1.1.-)	0.06	-	cyt	0					143
Q6L5F6 UniProt NPD GO	PIN3B_ORYSA	Putative auxin efflux carrier component 3b (OsPIN3b)	0.06	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				590
Q9Y885 UniProt NPD GO	TOXF_COCCA	Putative branched-chain-amino-acid aminotransferase TOXF (EC 2.6.1.42)	0.06	-	nuc	0					357
P45961 UniProt NPD GO	CEX2_CAEEL	Putative calcium-binding protein cex-2	0.06	-	cyt	0					166
P0C155 UniProt NPD GO	CBPS2_YEAST	Putative carboxypeptidase YOL153C (EC 3.4.17.-)	0.06	-	cyt	0	Membrane; single-pass type II membrane protein (Potential)				581
P80533 UniProt NPD GO	CATL9_FASHE	Putative cathepsin-like enzyme (EC 3.4.22.-) (Newly excysted juvenile protein 9) (Fragment)	0.06	-		0					16
Q8H0W9 UniProt NPD GO	CAP17_ARATH	Putative clathrin assembly protein At5g10410	0.06	-	nuc	0					338
O17624 UniProt NPD GO	C13B1_CAEEL	Putative cytochrome P450 cyp-13B1 (EC 1.14.-.-)	0.06	-	end	1 *					527
Q9FHB3 UniProt NPD GO	FBRL3_ARATH	Putative fibrillarin-3	0.06	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				292
Q00223 UniProt NPD GO	XP4_XENLA	Putative gastrointestinal growth factor xP4 precursor (TFF p4.1)	0.06	-	nuc	0	Secreted protein				224
Q9ZU91 UniProt NPD GO	E133_ARATH	Putative glucan endo-1,3-beta-glucosidase 3 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			501
P58953 UniProt NPD GO	GR22E_DROME	Putative gustatory receptor 22e	0.06	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			389
Q8IRL8 UniProt NPD GO	GR09A_DROME	Putative gustatory receptor 9a	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			341
Q5B1Z0 UniProt NPD GO	CCPR2_EMENI	Putative heme-binding peroxidase (EC 1.11.1.-)	0.06	-	cyt	0					312
Q8TFG1 UniProt NPD GO	GHTX_SCHPO	Putative high-affinity hexose transporter C1348.14c	0.06	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				518
P82729 UniProt NPD GO	LCR14_ARATH	Putative low-molecular-weight cysteine-rich protein LCR14 precursor	0.06	-	gol	1 *					79
P82719 UniProt NPD GO	LCR4_ARATH	Putative low-molecular-weight cysteine-rich protein LCR4 precursor	0.06	-	exc	1 *					81
P82761 UniProt NPD GO	LCR46_ARATH	Putative low-molecular-weight cysteine-rich protein LCR46 precursor	0.06	-	exc	1 *					91
P82772 UniProt NPD GO	LCR58_ARATH	Putative low-molecular-weight cysteine-rich protein LCR58 precursor	0.06	-	exc	1 *					127
Q9P6I3 UniProt NPD GO	YHG7_SCHPO	Putative mannan endo-1,6-alpha-mannosidase C1198.07c precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-man ...	0.06	-	end	2					507
Q18411 UniProt NPD GO	NTP1_CAEEL	Putative nucleoside-triphosphatase ntp-1 (EC 3.6.1.15)	0.06	-	nuc	1					485
P82983 UniProt NPD GO	OR65B_DROME	Putative odorant receptor 65b	0.06	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			406
P52570 UniProt NPD GO	TSA_ONCVO	Putative peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Thiol-specific antioxidant)	0.06	-	nuc	0					232
Q8VXB1 UniProt NPD GO	HAK12_ORYSA	Putative potassium transporter 12 (OsHAK12)	0.06	-	end	13 *	Membrane; multi-pass membrane protein (By similarity)				793
O43531 UniProt NPD GO	RG141_HUMAN	Putative protein RIG-like 14-1	0.06	-	cyt	0					85

You are viewing entries 73001 to 73050 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.