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
Q00673 UniProt NPD GO	NUGM_CANMA	Probable NADH-ubiquinone oxidoreductase 30.4 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1 ...	0.30	-	mit	0	Mitochondrion; mitochondrial inner membrane				276
Q08295 UniProt NPD GO	MALX4_YEAST	Probable alpha-glucosidase YOL157C (EC 3.2.1.20) (Maltase)	0.30	-	cyt	0					589
P60839 UniProt NPD GO	DRL2_ARATH	Probable disease resistance protein At1g12290	0.30	-	cyt	0					884
Q9FG91 UniProt NPD GO	DRL32_ARATH	Probable disease resistance protein At5g43730	0.30	-	mit	0					848
Q7S565 UniProt NPD GO	COQ1_NEUCR	Probable hexaprenyl pyrophosphate synthetase, mitochondrial precursor (EC 2.5.1.-) (HPS)	0.30	-	mit	0	Mitochondrion (By similarity)				449
Q9XWP6 UniProt NPD GO	LSD1_CAEEL	Probable lysine-specific histone demethylase 1 (EC 1.-.-.-) (Suppressor of presenilin 5) (P110b homo ...	0.30	-	cyt	0	Nucleus (Probable)				770
P38130 UniProt NPD GO	KTR3_YEAST	Probable mannosyltransferase KTR3 (EC 2.4.1.131)	0.30	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				404
Q76IC6 UniProt NPD GO	ZDH23_RAT	Probable palmitoyltransferase ZDHHC23 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 23) ( ...	0.30	-	end	6	Membrane; multi-pass membrane protein (Potential). Neuronal soma and dendrites				429
Q93Z04 UniProt NPD GO	PEL13_ARATH	Probable pectate lyase 13 precursor (EC 4.2.2.2) (Powdery mildew-resistant mutant 6) (Powdery mildew ...	0.30	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	anchored to membrane [TAS]			501
P70704 UniProt NPD GO	AT8A1_MOUSE	Probable phospholipid-transporting ATPase IA (EC 3.6.3.1) (Chromaffin granule ATPase II) (ATPase cla ...	0.30	-	end	8	Integral membrane protein. Chromaffin granules (By similarity)				1149
Q9MUN2 UniProt NPD GO	RRP3_MESVI	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.30	-	mit	0	Plastid; chloroplast				123
Q9N5M2 UniProt NPD GO	PFD2_CAEEL	Probable prefoldin subunit 2	0.30	-	nuc	0					141
Q9JJJ7 UniProt NPD GO	PORCN_MOUSE	Probable protein-cysteine N-palmitoyltransferase porcupine (EC 2.3.1.-) (mPORC)	0.30	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			461
P34265 UniProt NPD GO	KIN31_CAEEL	Probable tyrosine-protein kinase kin-31 (EC 2.7.10.2)	0.30	-	mit	0					437
P43001 UniProt NPD GO	PRL_BUFJA	Prolactin (PRL) (Fragment)	0.30	-	cyt	0	Secreted protein				134
Q28172 UniProt NPD GO	PRLR_BOVIN	Prolactin receptor precursor (PRL-R)	0.30	-	exc	2 *	Membrane; single-pass type I membrane protein	cell surface [ISS]			581
P51525 UniProt NPD GO	PF12_PIG	Prophenin-2 precursor (PF-2) (PR-2) (C12) (Prophenin-1-like)	0.30	-	nuc	1 *	Secreted protein				228
Q62969 UniProt NPD GO	PTGIS_RAT	Prostacyclin synthase (EC 5.3.99.4) (Prostaglandin I2 synthase)	0.30	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				501
P23219 UniProt NPD GO	PGH1_HUMAN	Prostaglandin G/H synthase 1 precursor (EC 1.14.99.1) (Cyclooxygenase-1) (COX-1) (Prostaglandin-endo ...	0.30	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [ISS] microsome [ISS] nucleus [ISS]	176805		599
P22437 UniProt NPD GO	PGH1_MOUSE	Prostaglandin G/H synthase 1 precursor (EC 1.14.99.1) (Cyclooxygenase-1) (COX-1) (Prostaglandin-endo ...	0.30	-	mit	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [IDA] microsome [IDA]			602
P12881 UniProt NPD GO	PSA1_DROME	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome 35 kDa subunit) (PROS-Dm35)	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				279
Q96PS1 UniProt NPD GO	CC024_HUMAN	Protein C3orf24	0.30	-	nuc	0					177
Q32KZ5 UniProt NPD GO	CC024_BOVIN	Protein C3orf24 homolog	0.30	-	nuc	0					178
Q5TGI0 UniProt NPD GO	CF168_HUMAN	Protein C6orf168	0.30	-	mit	0					409
Q9CR26 UniProt NPD GO	CF055_MOUSE	Protein C6orf55 homolog	0.30	-	nuc	0					309
Q08685 UniProt NPD GO	CLP1_YEAST	Protein CLP1	0.30	-	cyt	0	Nucleus (Probable)	mRNA cleavage factor complex [IPI]			445
P13665 UniProt NPD GO	EN16_STRPU	Protein ENDO16 (Fragment)	0.30	-	nuc	0					265
Q6DGM1 UniProt NPD GO	F100A_BRARE	Protein FAM100A	0.30	-	nuc	0					155
Q9DAN6 UniProt NPD GO	F112B_MOUSE	Protein FAM112B	0.30	-	nuc	0					167
Q06674 UniProt NPD GO	HIM1_YEAST	Protein HIM1 (High induction of mutagenesis protein 1)	0.30	-	nuc	0					414
P35844 UniProt NPD GO	KES1_YEAST	Protein KES1 (Oxysterol-binding protein homolog 4)	0.30	-	nuc	0		cytoplasm [IDA] extrinsic to membrane [IDA] Golgi membrane [IDA]		1ZI7	434
O75143 UniProt NPD GO	K0652_HUMAN	Protein KIAA0652	0.30	-	nuc	0					517
Q58DG1 UniProt NPD GO	MYG1_BOVIN	Protein MYG1	0.30	-	mit	0					381
P91891 UniProt NPD GO	MO25_DROME	Protein Mo25 (dMo25)	0.30	-	cyt	0					339
P40354 UniProt NPD GO	NTA1_YEAST	Protein N-terminal amidase (EC 3.5.1.-) (NT-amidase)	0.30	-	mit	0		mitochondrion [IDA]			457
P51609 UniProt NPD GO	NOV_XENLA	Protein NOV homolog precursor (Xnov)	0.30	-	exc	0	Secreted protein				343
Q5R4V2 UniProt NPD GO	RUFY3_PONPY	Protein RUFY3	0.30	-	nuc	0					469
Q9D394 UniProt NPD GO	RUFY3_MOUSE	Protein RUFY3 (Rap2-interacting protein x) (RIPx)	0.30	-	nuc	0				2CXL	469
Q99584 UniProt NPD GO	S10AD_HUMAN	Protein S100-A13 (S100 calcium-binding protein A13)	0.30	-	cyt	0			601989	1YUU	98
O82088 UniProt NPD GO	SELFP_LYCES	Protein SELF-PRUNING	0.30	-	cyt	0	Cytoplasm (By similarity)				175
Q9WUD6 UniProt NPD GO	WNT8B_MOUSE	Protein Wnt-8b precursor	0.30	-	exc	0	Secreted protein; extracellular space; extracellular matrix				350
P22815 UniProt NPD GO	BOSS_DROME	Protein bride of sevenless precursor	0.30	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS] microvillus [IDA]			896
Q24337 UniProt NPD GO	ER_DROME	Protein enhancer of rudimentary	0.30	-	nuc	0					104
Q25515 UniProt NPD GO	KRUP_MANSE	Protein krueppel (Fragment)	0.30	-	nuc	0	Nucleus (Probable)				76
Q02035 UniProt NPD GO	KRUP_PSYCI	Protein krueppel (Fragment)	0.30	-	nuc	0	Nucleus (Probable)				74
Q2HJA4 UniProt NPD GO	PAR2_BOVIN	Proteinase-activated receptor 2 precursor (PAR-2) (Thrombin receptor-like 1) (Coagulation factor II ...	0.30	+	end	7 *	Membrane; multi-pass membrane protein (By similarity)				395
Q63768 UniProt NPD GO	CRK_RAT	Proto-oncogene C-crk (P38) (Adapter molecule crk)	0.30	-	nuc	0	Cytoplasm. Cell membrane. Translocated to the plasma membrane upon cell adhesion				304
Q9Y5I1 UniProt NPD GO	PCDAB_HUMAN	Protocadherin alpha 11 precursor (PCDH-alpha11)	0.30	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606317		949
Q9UN75 UniProt NPD GO	PCDAC_HUMAN	Protocadherin alpha 12 precursor (PCDH-alpha12)	0.30	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606318		941
Q5DRF2 UniProt NPD GO	PCDAC_PANTR	Protocadherin alpha 12 precursor (PCDH-alpha12)	0.30	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				941

You are viewing entries 40651 to 40700 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.