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
O78420 UniProt NPD GO	YCX1_GUITH	Hypothetical 15.1 kDa protein (ORF125)	0.24	-	nuc	0	Plastid; chloroplast				125
Q9MUQ8 UniProt NPD GO	YCF66_MESVI	Hypothetical 19.4 kDa protein ycf66 (RF66)	0.24	-	end	3 *	Plastid; chloroplast				170
Q9MUN5 UniProt NPD GO	YCX2_MESVI	Hypothetical 19.8 kDa protein in petA-petL intergenic region	0.24	-	mit	1	Plastid; chloroplast				167
P46315 UniProt NPD GO	YCF22_ANTSP	Hypothetical 23.3 kDa protein ycf22 (ORF 198)	0.24	-	cyt	0	Plastid; chloroplast				198
P38838 UniProt NPD GO	YHT4_YEAST	Hypothetical 30.6 kDa protein in ACT5-YCK1 intergenic region	0.24	-	nuc	0					269
O78449 UniProt NPD GO	YCF80_GUITH	Hypothetical 33.2 kDa protein ycf80	0.24	-	cyt	0	Plastid; chloroplast				282
P49530 UniProt NPD GO	YCF24_ODOSI	Hypothetical UPF0051 protein ycf24 (ORF486)	0.24	-	cyt	0	Plastid; chloroplast				486
P93301 UniProt NPD GO	M450_ARATH	Hypothetical mitochondrial protein AtMg00450 (ORF106b)	0.24	-	nuc	0	Mitochondrion (Potential)				106
P46556 UniProt NPD GO	YKG6_CAEEL	Hypothetical protein B0285.6 in chromosome III	0.24	-	end	9	Membrane; multi-pass membrane protein (Potential)				577
Q11078 UniProt NPD GO	YT61_CAEEL	Hypothetical protein B0563.1	0.24	-	nuc	0					187
P34283 UniProt NPD GO	YKK6_CAEEL	Hypothetical protein C02F5.6	0.24	-	cyt	0					450
Q11113 UniProt NPD GO	YX06_CAEEL	Hypothetical protein C03B1.6	0.24	-	exc	1 *					131
P34318 UniProt NPD GO	YKT7_CAEEL	Hypothetical protein C07A9.7	0.24	-	cyt	0					465
Q10313 UniProt NPD GO	YD61_SCHPO	Hypothetical protein C17G8.01c in chromosome I	0.24	-	cyt	0					787
Q09759 UniProt NPD GO	YA72_SCHPO	Hypothetical protein C24H6.02c in chromosome I	0.24	-	mit	0					175
Q9UUC2 UniProt NPD GO	YGR1_SCHPO	Hypothetical protein C365.01 in chromosome II	0.24	-	cyt	0					355
O74383 UniProt NPD GO	YNV8_SCHPO	Hypothetical protein C3H7.08c in chromosome II	0.24	-	mit	1 *					120
O74387 UniProt NPD GO	YNVC_SCHPO	Hypothetical protein C3H7.12 in chromosome II	0.24	-	nuc	0					287
O14171 UniProt NPD GO	YE54_SCHPO	Hypothetical protein C4D7.04c in chromosome I	0.24	-	cyt	0					264
Q9HDZ2 UniProt NPD GO	YKPC_SCHPO	Hypothetical protein C589.12 in chromosome I	0.24	+	end	19 *	Membrane; multi-pass membrane protein (Potential)				971
P41952 UniProt NPD GO	YLK4_CAEEL	Hypothetical protein D1044.4	0.24	-	nuc	0					103
P34527 UniProt NPD GO	YM66_CAEEL	Hypothetical protein K12H4.6	0.24	-	nuc	0					84
Q629J5 UniProt NPD GO	YRRC_CAEEL	Hypothetical protein R144.12	0.24	-	mit	2 *					333
P82640 UniProt NPD GO	SCR21_ARATH	Hypothetical protein SCRL21 precursor	0.24	-	nuc	1 *					109
Q22616 UniProt NPD GO	YNXA_CAEEL	Hypothetical protein T20G5.10 in chromosome III	0.24	-	nuc	0					129
P30637 UniProt NPD GO	YOU4_CAEEL	Hypothetical protein ZK637.4	0.24	-	nuc	0					95
P40415 UniProt NPD GO	YP13_DICDI	Hypothetical protein in protein P13 5'region (Fragment)	0.24	-	cyt	0					91
P38459 UniProt NPD GO	YMF16_MARPO	Hypothetical tatC-like protein ymf16 (ORF 244)	0.24	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				244
P48278 UniProt NPD GO	YCF38_CYAPA	Hypothetical transport permease ycf38	0.24	-	end	6 *	Plastid; cyanelle; cyanelle membrane; multi-pass membrane protein (By similarity)				290
Q22523 UniProt NPD GO	YCYL_CAEEL	Hypothetical zinc metalloproteinase T16A9.4 (EC 3.4.24.-)	0.24	-	end	1 *	Membrane; single-pass type II membrane protein (Potential)				769
P69494 UniProt NPD GO	CXI_CONCE	I-superfamily conotoxin precursor	0.24	-	mit	1 *	Secreted protein (By similarity)				67
Q4W9B9 UniProt NPD GO	ISN1_ASPFU	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.24	-	mit	0					450
P01660 UniProt NPD GO	KV3H_MOUSE	Ig kappa chain V-III region PC 3741/TEPC 111	0.24	-	nuc	0					111
P01637 UniProt NPD GO	KV5E_MOUSE	Ig kappa chain V-V region T1 precursor	0.24	-	exc	0					128
P04945 UniProt NPD GO	KV6K_MOUSE	Ig kappa chain V-VI region NQ2-6.1	0.24	-	nuc	0					108
Q8N126 UniProt NPD GO	IGS4B_HUMAN	Immunoglobulin superfamily member 4B precursor (Nectin-like protein 1) (TSLC1-like protein 1) (Synap ...	0.24	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein (By similarity). Localized at ...		609743	1Z9M	398
Q9CQY5 UniProt NPD GO	IAG2_MOUSE	Implantation-associated protein precursor (IAP) (Magnesium transporter protein 1) (MagT1)	0.24	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	oligosaccharyl transferase complex [ISS]			335
P14777 UniProt NPD GO	INF24_UROAP	Infection structure-specific protein 24	0.24	-	nuc	1 *					150
P04087 UniProt NPD GO	INHA_PIG	Inhibin alpha chain precursor	0.24	-	end	0	Secreted protein	extracellular region [ISS]			364
P17491 UniProt NPD GO	INHBB_RAT	Inhibin beta B chain precursor (Activin beta-B chain)	0.24	-	end	0	Secreted protein (By similarity)				411
Q8BGA9 UniProt NPD GO	OXA1L_MOUSE	Inner membrane protein OXA1L, mitochondrial precursor (Oxidase assembly 1-like protein) (OXA1-like p ...	0.24	-	end	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			433
P40060 UniProt NPD GO	IES5_YEAST	Ino eighty subunit 5	0.24	-	nuc	0	Nucleus	nucleus [IDA]			125
P07456 UniProt NPD GO	IGF2_BOVIN	Insulin-like growth factor II precursor (IGF-II) (Erythrotropin)	0.24	-	exc	0	Secreted protein				179
P21743 UniProt NPD GO	IBP1_RAT	Insulin-like growth factor-binding protein 1 precursor (IGFBP-1) (IBP-1) (IGF-binding protein 1)	0.24	-	nuc	0	Secreted protein				272
Q7Z3F1 UniProt NPD GO	GP155_HUMAN	Integral membrane protein GPR155 (G-protein coupled receptor PGR22)	0.24	-	end	15 *	Membrane; multi-pass membrane protein				870
Q07441 UniProt NPD GO	ITB5_PAPCY	Integrin beta-5 (Fragment)	0.24	-	cyt	1	Membrane; single-pass type I membrane protein				655
P57043 UniProt NPD GO	ILK2_HUMAN	Integrin-linked protein kinase 2 (EC 2.7.11.1) (ILK-2)	0.24	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]			452
O02668 UniProt NPD GO	ITIH2_PIG	Inter-alpha-trypsin inhibitor heavy chain H2 precursor (ITI heavy chain H2) (Inter-alpha-inhibitor h ...	0.24	-	exc	0					935
Q61704 UniProt NPD GO	ITIH3_MOUSE	Inter-alpha-trypsin inhibitor heavy chain H3 precursor (ITI heavy chain H3) (Inter-alpha-inhibitor h ...	0.24	-	vac	0					886
Q28125 UniProt NPD GO	ICAM3_BOVIN	Intercellular adhesion molecule 3 precursor (ICAM-3) (CD50 antigen)	0.24	-	end	1 *	Membrane; single-pass type I membrane protein				544

You are viewing entries 46401 to 46450 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.