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
Q09626 UniProt NPD GO	ILB1_CAEEL	Probable insulin-like peptide beta-type 1 precursor	0.34	-	exc	0	Secreted protein (Potential)				106
Q9ULC8 UniProt NPD GO	ZDHC8_HUMAN	Probable palmitoyltransferase ZDHHC8 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 8) (DH ...	0.34	-	mit	4 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (Potential)		608784		765
Q8NB49 UniProt NPD GO	AT11C_HUMAN	Probable phospholipid-transporting ATPase IG (EC 3.6.3.1) (ATPase class I type 11C) (ATPase IG) (ATP ...	0.34	-	end	7	Membrane; multi-pass membrane protein		300516		1132
Q7PC85 UniProt NPD GO	PDR10_ARATH	Probable pleiotropic drug resistance protein 10	0.34	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1418
Q7PC86 UniProt NPD GO	PDR7_ARATH	Probable pleiotropic drug resistance protein 7	0.34	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1442
Q12265 UniProt NPD GO	KPR5_YEAST	Probable ribose-phosphate pyrophosphokinase 5 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase ...	0.34	-	nuc	0		cytoplasm [IDA]			496
Q9LQQ8 UniProt NPD GO	RLCK7_ARATH	Probable serine/threonine-protein kinase RLCKVII (EC 2.7.11.1)	0.34	-	nuc	0					423
Q18678 UniProt NPD GO	SYS_CAEEL	Probable seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.34	-	cyt	0					487
Q3E9B8 UniProt NPD GO	WBC24_ARATH	Probable white-brown complex homolog protein 24	0.34	-	end	5	Membrane; multi-pass membrane protein (By similarity)				624
Q9IA08 UniProt NPD GO	GON2_DICLA	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.34	-	end	0	Secreted protein				85
O35129 UniProt NPD GO	PHB2_MOUSE	Prohibitin-2 (B-cell receptor-associated protein BAP37) (Repressor of estrogen receptor activity)	0.34	-	mit	0	Mitochondrion; mitochondrial inner membrane. Cytoplasm. Nucleus. Also cytoplasmic and nuclear	mitochondrial inner membrane [IDA] mitochondrion [IDA] nucleus [IDA]			299
Q99623 UniProt NPD GO	PHB2_HUMAN	Prohibitin-2 (B-cell receptor-associated protein BAP37) (Repressor of estrogen receptor activity) (D ...	0.34	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Cytoplasm (By similarity). Nucleus (By ...	mitochondrial inner membrane [ISS] nucleus [ISS]			299
O62819 UniProt NPD GO	PRL_MONDO	Prolactin precursor (PRL)	0.34	-	exc	0	Secreted protein				228
Q8IVL5 UniProt NPD GO	P3H2_HUMAN	Prolyl 3-hydroxylase 2 precursor (EC 1.14.11.7) (Leprecan-like protein 1) (Myxoid liposarcoma-associ ...	0.34	-	end	0	Endoplasmic reticulum. Golgi apparatus				708
O35074 UniProt NPD GO	PTGIS_MOUSE	Prostacyclin synthase (EC 5.3.99.4) (Prostaglandin I2 synthase)	0.34	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				501
Q9NDA2 UniProt NPD GO	PSA7_TRYBB	Proteasome subunit alpha type 7 (EC 3.4.25.1) (20S proteasome subunit alpha-4)	0.34	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				247
Q5BC71 UniProt NPD GO	AF9_EMENI	Protein AF-9 homolog	0.34	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				275
Q9H761 UniProt NPD GO	CN139_HUMAN	Protein C14orf139	0.34	-	nuc	0					190
P05526 UniProt NPD GO	C2_OXYNO	Protein C2	0.34	-	nuc	0					82
Q9BTX7 UniProt NPD GO	CT121_HUMAN	Protein C20orf121	0.34	-	cyt	0					342
P58512 UniProt NPD GO	CU067_HUMAN	Protein C21orf67	0.34	-	nuc	0					204
Q8K215 UniProt NPD GO	CF149_MOUSE	Protein C6orf149 homolog	0.34	-	nuc	0					91
Q9NP79 UniProt NPD GO	CF055_HUMAN	Protein C6orf55 (Dopamine-responsive protein DRG-1)	0.34	-	nuc	0					307
Q80X86 UniProt NPD GO	CF081_MOUSE	Protein C6orf81 homolog	0.34	-	mit	0					340
P19336 UniProt NPD GO	CEF10_CHICK	Protein CEF-10 precursor	0.34	-	exc	0	Secreted protein (Probable)				375
Q9H8M1 UniProt NPD GO	CQ10B_HUMAN	Protein COQ10 B, mitochondrial precursor	0.34	-	mit	0	Mitochondrion (Potential)				238
Q8N9T2 UniProt NPD GO	CX042_HUMAN	Protein CXorf42	0.34	-	mit	0					121
Q8TB05 UniProt NPD GO	F100A_HUMAN	Protein FAM100A	0.34	-	nuc	0					177
Q6P3B2 UniProt NPD GO	F100A_MOUSE	Protein FAM100A	0.34	-	nuc	0					176
Q6AXN0 UniProt NPD GO	F100A_RAT	Protein FAM100A	0.34	-	nuc	0					176
Q6AX60 UniProt NPD GO	PTHB1_XENLA	Protein PTHB1 (Parathyroid hormone-responsive B1 gene protein homolog)	0.34	-	cyt	0					849
Q6CJ97 UniProt NPD GO	SEY1_KLULA	Protein SEY1	0.34	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				786
Q12038 UniProt NPD GO	SNI1_YEAST	Protein SNI1 (Suppressor of RHO3 protein 7)	0.34	-	nuc	0		cytosol [IDA] plasma membrane [IDA]			1033
P32867 UniProt NPD GO	SSO1_YEAST	Protein SSO1	0.34	-	cyt	1	Membrane; single-pass type IV membrane protein (Potential)	integral to plasma membrane [TAS]		1FIO	290
Q6UW78 UniProt NPD GO	U655_HUMAN	Protein UNQ655/PRO1286 precursor	0.34	-	mit	1 *	Secreted protein (Probable)				93
Q9V4M2 UniProt NPD GO	DPLD_DROME	Protein dappled	0.34	-	nuc	0					832
Q921X9 UniProt NPD GO	PDIA5_MOUSE	Protein disulfide-isomerase A5 precursor (EC 5.3.4.1) (Protein disulfide isomerase-related protein)	0.34	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				517
Q06548 UniProt NPD GO	APK1A_ARATH	Protein kinase APK1A, chloroplast precursor (EC 2.7.11.1)	0.34	+	cyt	0	Plastid; chloroplast (Potential)				410
Q04759 UniProt NPD GO	KPCT_HUMAN	Protein kinase C theta type (EC 2.7.11.13) (nPKC-theta)	0.34	-	cyt	0		intracellular [NAS]	600448	1XJD	706
Q92832 UniProt NPD GO	NELL1_HUMAN	Protein kinase C-binding protein NELL1 precursor (NEL-like protein 1) (Nel-related protein 1)	0.34	-	nuc	0	Secreted protein (By similarity)		602319		810
P10506 UniProt NPD GO	BYR1_SCHPO	Protein kinase byr1 (EC 2.7.12.2) (MAPK kinase) (MAPKK)	0.34	-	mit	0					340
Q8N2H9 UniProt NPD GO	PELI3_HUMAN	Protein pellino homolog 3 (Pellino-3)	0.34	-	nuc	0			609827		469
P22194 UniProt NPD GO	SDS22_SCHPO	Protein phosphatase 1 regulatory subunit SDS22	0.34	-	nuc	0	Nucleus	protein serine/threonine phosphatase complex [TAS]			332
Q2T9V7 UniProt NPD GO	PREY_BOVIN	Protein preY, mitochondrial precursor	0.34	-	mit	0	Mitochondrion (Potential)				114
P19339 UniProt NPD GO	SXL_DROME	Protein sex-lethal	0.34	-	nuc	0				3SXL	354
Q9VQS7 UniProt NPD GO	SOB_DROME	Protein sister of odd and bowel	0.34	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			578
Q01083 UniProt NPD GO	SPITZ_DROME	Protein spitz precursor	0.34	+	end	1	Cell membrane; single-pass type I membrane protein. Endoplasmic reticulum; endoplasmic reticulum mem ...	endoplasmic reticulum [IDA] extracellular region [TAS] Golgi apparatus [IGI] integral to membrane [NAS]			234
O42852 UniProt NPD GO	SEC20_SCHPO	Protein transport protein sec20	0.34	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				226
P49221 UniProt NPD GO	TGM4_HUMAN	Protein-glutamine gamma-glutamyltransferase 4 (EC 2.3.2.13) (Transglutaminase-4) (TGase-4) (Prostate ...	0.34	-	cyt	0			600585		684
P00536 UniProt NPD GO	MOS_MOUSE	Proto-oncogene serine/threonine-protein kinase mos (EC 2.7.11.1) (c-mos) (Oocyte maturation factor m ...	0.34	-	cyt	0					390

You are viewing entries 37001 to 37050 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.