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
P27071 UniProt NPD GO	RR14_EPIVI	Plastid 30S ribosomal protein S14	0.50	-	nuc	0	Plastid				100
P34832 UniProt NPD GO	RR7_CUSRE	Plastid 30S ribosomal protein S7	0.50	-	nuc	0	Plastid				155
O63057 UniProt NPD GO	RR7_LATCL	Plastid 30S ribosomal protein S7	0.50	-	nuc	0	Plastid				155
Q9TJQ9 UniProt NPD GO	RR7_PROWI	Plastid 30S ribosomal protein S7	0.50	-	nuc	0	Plastid				156
Q9SX22 UniProt NPD GO	RRP31_ARATH	Plastid-specific 30S ribosomal protein 3-1, chloroplast precursor (PSRP-3 1)	0.50	-	mit	0	Plastid; chloroplast (By similarity)				166
Q9NYI0 UniProt NPD GO	EFA6R_HUMAN	Pleckstrin and Sec7 domain-containing protein 3 (Exchange factor for ADP-ribosylation factor guanine ...	0.50	-	nuc	0					534
Q9WUC8 UniProt NPD GO	PLRG1_RAT	Pleiotropic regulator 1	0.50	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				514
O60486 UniProt NPD GO	PLXC1_HUMAN	Plexin-C1 precursor (Virus-encoded semaphorin protein receptor) (CD232 antigen)	0.50	-	nuc	2	Membrane; single-pass type I membrane protein (Potential)	plasma membrane [NAS]	604259		1568
P09874 UniProt NPD GO	PARP1_HUMAN	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase 1) (Pol ...	0.50	+	nuc	0	Nucleus	nucleus [TAS]	173870	2CS2	1013
Q8IXQ6 UniProt NPD GO	PARP9_HUMAN	Poly [ADP-ribose] polymerase 9 (EC 2.4.2.30) (PARP-9) (B aggressive lymphoma protein)	0.50	-	mit	0	Nucleus	nucleus [TAS]			854
Q14435 UniProt NPD GO	GALT3_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 3 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.50	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Resides pr ...	integral to membrane [TAS] membrane fraction [TAS]	601756		633
Q43316 UniProt NPD GO	HEM3_ARATH	Porphobilinogen deaminase, chloroplast precursor (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) ...	0.50	-	mit	0	Plastid; chloroplast				382
Q39128 UniProt NPD GO	KAT1_ARATH	Potassium channel KAT1	0.50	-	end	6	Membrane; multi-pass membrane protein				677
Q8TDN2 UniProt NPD GO	KCNV2_HUMAN	Potassium voltage-gated channel subfamily V member 2 (Voltage-gated potassium channel subunit Kv8.2) ...	0.50	-	end	3	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. Has to be associa ...		607604		545
Q6FP02 UniProt NPD GO	CWC25_CANGA	Pre-mRNA-splicing factor CWC25	0.50	-	nuc	0	Nucleus (By similarity)				176
Q6FKZ2 UniProt NPD GO	SLT11_CANGA	Pre-mRNA-splicing factor SLT11	0.50	-	nuc	0	Nucleus (By similarity)				364
Q32743 UniProt NPD GO	SECA_OLILU	Preprotein translocase secA subunit	0.50	-	cyt	0	Plastid; chloroplast				884
P42520 UniProt NPD GO	RS17_DICDI	Probable 40S ribosomal protein S17	0.50	-	nuc	0					134
Q6CCH0 UniProt NPD GO	TAH18_YARLI	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.50	-	cyt	0					688
Q12181 UniProt NPD GO	TAH18_YEAST	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.50	-	mit	0					623
O14123 UniProt NPD GO	NAH2_SCHPO	Probable Na(+)/H(+) antiporter C3A11.09	0.50	+	end	11 *	Membrane; multi-pass membrane protein (Potential)				759
Q93WU7 UniProt NPD GO	WRK58_ARATH	Probable WRKY transcription factor 58 (WRKY DNA-binding protein 58)	0.50	-	nuc	0	Nucleus (Potential)				423
Q9MAG6 UniProt NPD GO	RP8L2_ARATH	Probable disease resistance RPP8-like protein 2	0.50	-	cyt	0					1271
Q10415 UniProt NPD GO	PMIP_SCHPO	Probable mitochondrial intermediate peptidase, mitochondrial precursor (EC 3.4.24.59) (MIP)	0.50	-	mit	0	Mitochondrion; mitochondrial matrix				762
Q2THX1 UniProt NPD GO	ZDHC5_PANTR	Probable palmitoyltransferase ZDHHC5 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 5) (DH ...	0.50	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				715
Q9C0B5 UniProt NPD GO	ZDHC5_HUMAN	Probable palmitoyltransferase ZDHHC5 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 5) (DH ...	0.50	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				715
O43861 UniProt NPD GO	ATP9B_HUMAN	Probable phospholipid-transporting ATPase IIB (EC 3.6.3.1)	0.50	-	end	9 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			1095
P98195 UniProt NPD GO	ATP9B_MOUSE	Probable phospholipid-transporting ATPase IIB (EC 3.6.3.1)	0.50	+	end	10	Membrane; multi-pass membrane protein				1095
Q5JMF2 UniProt NPD GO	ABIL5_ORYSA	Probable protein ABIL5 (Abl interactor-like protein 5)	0.50	-	nuc	0					254
P12420 UniProt NPD GO	PRL_HORSE	Prolactin precursor (PRL)	0.50	-	exc	0	Secreted protein				229
Q9GKN8 UniProt NPD GO	PRELP_BOVIN	Prolargin precursor (Proline-arginine-rich end leucine-rich repeat protein)	0.50	+	mit	0	Secreted protein; extracellular space; extracellular matrix				381
Q6JHU7 UniProt NPD GO	P3H2_CHICK	Prolyl 3-hydroxylase 2 precursor (EC 1.14.11.7) (Leprecan-like protein 1)	0.50	-	end	0	Endoplasmic reticulum. Golgi apparatus (By similarity)				694
P38872 UniProt NPD GO	ADY1_YEAST	Prospore formation at selected spindle poles protein 1 (Accumulates dyads protein 1)	0.50	-	nuc	0	Nucleus. Nuclear in mononucleate meiotic cells. May not be localized to the spindle pole body or pro ...				237
Q62928 UniProt NPD GO	PE2R2_RAT	Prostaglandin E2 receptor, EP2 subtype (Prostanoid EP2 receptor) (PGE receptor, EP2 subtype)	0.50	-	end	7 *	Membrane; multi-pass membrane protein				357
Q95KZ0 UniProt NPD GO	PE2R4_PANTR	Prostaglandin E2 receptor, EP4 subtype (Prostanoid EP4 receptor) (PGE receptor, EP4 subtype)	0.50	-	end	6 *	Membrane; multi-pass membrane protein				490
P43114 UniProt NPD GO	PE2R4_RAT	Prostaglandin E2 receptor, EP4 subtype (Prostanoid EP4 receptor) (PGE receptor, EP4 subtype)	0.50	-	end	6 *	Membrane; multi-pass membrane protein				488
P41540 UniProt NPD GO	TKN1_RABIT	Protachykinin 1 precursor (PPT) [Contains: Substance P; Neurokinin A (NKA) (Substance K) (Neuromedin ...	0.50	-	exc	0	Secreted protein				115
Q4R4V3 UniProt NPD GO	PSME3_MACFA	Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) ( ...	0.50	-	cyt	0					254
P61291 UniProt NPD GO	PSME3_PIG	Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) ( ...	0.50	-	cyt	0					254
P61289 UniProt NPD GO	PSME3_HUMAN	Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) ( ...	0.50	-	cyt	0			605129		254
P61290 UniProt NPD GO	PSME3_MOUSE	Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) ( ...	0.50	-	cyt	0					254
Q8R3C0 UniProt NPD GO	CJ119_MOUSE	Protein C10orf119 homolog	0.50	-	nuc	0					642
Q9Y7P6 UniProt NPD GO	YCI2_SCHPO	Protein C1902.02 in chromosome III	0.50	-	nuc	0	Cytoplasm	barrier septum [IDA] cell tip [IDA]			574
Q5FVR6 UniProt NPD GO	CC026_RAT	Protein C3orf26 homolog	0.50	-	nuc	0					276
Q53FE4 UniProt NPD GO	CD017_HUMAN	Protein C4orf17	0.50	-	nuc	0					359
Q6MG51 UniProt NPD GO	CF047_RAT	Protein C6orf47 homolog	0.50	-	end	0					293
Q8IYX7 UniProt NPD GO	CI138_HUMAN	Protein C9orf138	0.50	-	nuc	0					474
Q8MLL3 UniProt NPD GO	COQ10_DROME	Protein COQ10, mitochondrial precursor	0.50	-	nuc	0	Mitochondrion (Potential)	mitochondrial inner membrane [ISS]			242
P12805 UniProt NPD GO	G10_XENLA	Protein G10	0.50	-	nuc	0	Nucleus (Potential)				144
Q12768 UniProt NPD GO	K0196_HUMAN	Protein KIAA0196	0.50	-	nuc	0					1159

You are viewing entries 25151 to 25200 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.