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
Q9M156 UniProt NPD GO	HQGT_ARATH	Probable hydroquinone glucosyltransferase (EC 2.4.1.218) (Arbutin synthase)	0.10	-	cyt	0					480
Q60EJ6 UniProt NPD GO	GH34_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.4 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.10	-	cyt	0					629
O13642 UniProt NPD GO	LIPA_SCHPO	Probable lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthetase)	0.10	-	mit	0	Mitochondrion (By similarity)				370
Q74ZU6 UniProt NPD GO	ARX1_ASHGO	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.10	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				591
Q6BI90 UniProt NPD GO	ARX1_DEBHA	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.10	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				564
Q9VY28 UniProt NPD GO	RT25_DROME	Probable mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25)	0.10	-	cyt	0	Mitochondrion (By similarity)				167
O13656 UniProt NPD GO	TOM40_SCHPO	Probable mitochondrial import receptor subunit tom40 (Translocase of outer membrane 40 kDa subunit)	0.10	-	mit	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				344
Q9ZU25 UniProt NPD GO	MPPA1_ARATH	Probable mitochondrial-processing peptidase alpha subunit 1, mitochondrial precursor (EC 3.4.24.64) ...	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				503
O04514 UniProt NPD GO	OPT2_ARATH	Probable oligopeptide transporter 2 (AtOPT2)	0.10	-	end	13 *	Membrane; multi-pass membrane protein (Probable)				722
Q969W1 UniProt NPD GO	ZDH16_HUMAN	Probable palmitoyltransferase ZDHHC16 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 16) ( ...	0.10	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				377
Q4R7E2 UniProt NPD GO	ZDH16_MACFA	Probable palmitoyltransferase ZDHHC16 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 16) ( ...	0.10	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				377
P11706 UniProt NPD GO	IPK1_ANGAN	Probable pancreatic secretory proteinase inhibitor (PSTI type)	0.10	-	nuc	0	Secreted protein				61
Q9P380 UniProt NPD GO	PTR2_SCHPO	Probable peptide transporter ptr2 (Peptide permease ptr2)	0.10	-	end	10	Membrane; multi-pass membrane protein (Probable)				618
O76387 UniProt NPD GO	PTH2_CAEEL	Probable peptidyl-tRNA hydrolase 2 (EC 3.1.1.29) (PTH 2)	0.10	-	nuc	0					316
Q9VTE5 UniProt NPD GO	PFD2_DROME	Probable prefoldin subunit 2	0.10	-	cyt	0					143
Q17435 UniProt NPD GO	PFD4_CAEEL	Probable prefoldin subunit 4	0.10	-	nuc	0					126
Q9M4C4 UniProt NPD GO	PFD4_AVEFA	Probable prefoldin subunit 4 (VIP3 protein)	0.10	-	cyt	0					126
O65595 UniProt NPD GO	KPYC_ARATH	Probable pyruvate kinase, cytosolic isozyme (EC 2.7.1.40) (PK)	0.10	-	cyt	0	Cytoplasm (By similarity)				497
Q9LH76 UniProt NPD GO	RHM3_ARATH	Probable rhamnose biosynthetic enzyme 3 (EC 4.2.1.-) (EC 1.1.1.-)	0.10	-	cyt	0					664
Q20496 UniProt NPD GO	GDIR_CAEEL	Probable rho GDP-dissociation inhibitor (Rho GDI)	0.10	-	nuc	0	Cytoplasm (By similarity)				191
Q944J0 UniProt NPD GO	SPCS1_ARATH	Probable signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit ...	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				92
O13750 UniProt NPD GO	SUCA_SCHPO	Probable succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succ ...	0.10	-	mit	0	Mitochondrion (By similarity)				331
Q757U3 UniProt NPD GO	ETR1_ASHGO	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.10	-	mit	0	Mitochondrion (By similarity)				376
Q10171 UniProt NPD GO	UBLH1_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 1 (EC 3.1.2.15)	0.10	-	mit	0					222
P52484 UniProt NPD GO	UBC21_CAEEL	Probable ubiquitin-conjugating enzyme E2 21 (EC 6.3.2.19) (Ubiquitin-protein ligase 21) (Ubiquitin c ...	0.10	-	cyt	0					260
Q9SZR9 UniProt NPD GO	WBC9_ARATH	Probable white-brown complex homolog protein 9	0.10	-	end	6	Membrane; multi-pass membrane protein (By similarity)				635
Q9M0D1 UniProt NPD GO	XTH19_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 19 precursor (EC 2.4.1.207) (At-XTH19) (X ...	0.10	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				277
Q9NZQ7 UniProt NPD GO	PDL1_HUMAN	Programmed cell death 1 ligand 1 precursor (Programmed death ligand 1) (PD-L1) (PDCD1 ligand 1) (B7 ...	0.10	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Intracellular membrane; si ...		605402		290
Q3T165 UniProt NPD GO	PHB_BOVIN	Prohibitin	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				272
P35232 UniProt NPD GO	PHB_HUMAN	Prohibitin	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)	integral to plasma membrane [IDA] mitochondrial inner membrane [TAS] nucleoplasm [IDA] nucleus [TAS]	176705	1LU7	272
P67779 UniProt NPD GO	PHB_RAT	Prohibitin	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane				272
P67778 UniProt NPD GO	PHB_MOUSE	Prohibitin (B-cell receptor-associated protein 32) (BAP 32)	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			272
P02816 UniProt NPD GO	PIP_MOUSE	Prolactin-inducible protein homolog precursor (14 kDa submandibular gland protein) (SMGP) (Gross cys ...	0.10	-	vac	1 *	Secreted protein (Probable)				146
P17070 UniProt NPD GO	PCNA_ORYSA	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.10	-	mit	0	Nucleus				263
P05165 UniProt NPD GO	PCCA_HUMAN	Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit alpha) ( ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix		232000	2CQY	703
P37289 UniProt NPD GO	PF2R_BOVIN	Prostaglandin F2-alpha receptor (Prostanoid FP receptor) (PGF receptor) (PGF2 alpha receptor)	0.10	-	end	6 *	Membrane; multi-pass membrane protein				362
Q29562 UniProt NPD GO	PTGDS_URSAR	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.10	-	end	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [ISS] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			191
P08723 UniProt NPD GO	SPBP_RAT	Prostatic spermine-binding protein precursor (SBP)	0.10	-	exc	0					279
Q9BQR3 UniProt NPD GO	PRS27_HUMAN	Protease serine 27 precursor (EC 3.4.21.-) (Marapsin) (Pancreasin) (Channel-activating protease 2) ( ...	0.10	-	mit	0	Secreted protein		608018		290
Q9PVY6 UniProt NPD GO	PSA7A_XENLA	Proteasome subunit alpha type 7-A (EC 3.4.25.1) (Proteasome subunit alpha 4-A)	0.10	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				248
Q949P3 UniProt NPD GO	Y2734_ARATH	Protein At2g17340	0.10	-	cyt	0				1XFI	367
O80934 UniProt NPD GO	Y2766_ARATH	Protein At2g37660, chloroplast precursor	0.10	-	mit	0	Plastid; chloroplast (Potential)				325
Q96NT3 UniProt NPD GO	CV013_HUMAN	Protein C22orf13 (Protein LLN4)	0.10	-	cyt	0					239
O14290 UniProt NPD GO	YF14_SCHPO	Protein C9E9.04 in chromosome I	0.10	-	end	2 *	Membrane; multi-pass membrane protein				188
Q41261 UniProt NPD GO	CEN_ANTMA	Protein CENTRORADIALIS	0.10	-	cyt	0	Cytoplasm			1QOU	181
Q9H7F4 UniProt NPD GO	FA11B_HUMAN	Protein FAM11B	0.10	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				350
Q5RI15 UniProt NPD GO	FA36A_HUMAN	Protein FAM36A	0.10	-	nuc	0					118
Q6NSW5 UniProt NPD GO	FA45B_HUMAN	Protein FAM45B	0.10	-	cyt	0					357
Q3UZW7 UniProt NPD GO	FA86A_MOUSE	Protein FAM86A	0.10	-	cyt	0					335
Q15053 UniProt NPD GO	K0040_HUMAN	Protein KIAA0040	0.10	-	nuc	0					153

You are viewing entries 65051 to 65100 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.