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
Q5SSQ6 UniProt NPD GO	G7D_HUMAN	Protein G7d	0.36	-	mit	0					148
P0C199 UniProt NPD GO	KES1_USTMA	Protein KES1	0.36	-	cyt	0					383
Q5RDC8 UniProt NPD GO	K0528_PONPY	Protein KIAA0528 homolog	0.36	-	nuc	0					1000
O94964 UniProt NPD GO	K0889_HUMAN	Protein KIAA0889	0.36	-	nuc	0					518
Q9V447 UniProt NPD GO	KRH2_DROME	Protein Kr-h2	0.36	-	vac	4	Membrane; multi-pass membrane protein (Potential)				276
P53697 UniProt NPD GO	MNN9_CANAL	Protein MNN9	0.36	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				368
Q9CYI0 UniProt NPD GO	NJMU_MOUSE	Protein Njmu-R1	0.36	-	cyt	0					367
Q5EAB6 UniProt NPD GO	PMGT1_BOVIN	Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (POMGnT1)	0.36	-	end	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				660
Q6BJ08 UniProt NPD GO	OS9_DEBHA	Protein OS-9 homolog precursor	0.36	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				589
P54867 UniProt NPD GO	SLG1_YEAST	Protein SLG1 precursor (Cell wall integrity and stress response component 1)	0.36	-	exc	1		actin cap [IDA] membrane fraction [IDA] plasma membrane [IDA]			378
P22215 UniProt NPD GO	SLY41_YEAST	Protein SLY41	0.36	-	end	8	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			453
P49340 UniProt NPD GO	WNT1_BOMMO	Protein Wnt-1 precursor	0.36	-	mit	0	Secreted protein; extracellular space; extracellular matrix				392
Q24738 UniProt NPD GO	BOSS_DROVI	Protein bride of sevenless precursor	0.36	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				893
Q04903 UniProt NPD GO	PFTB_PEA	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.36	-	cyt	0					419
P49354 UniProt NPD GO	PFTA_HUMAN	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.36	-	cyt	0		cytoplasm [TAS]	134635	1TN6	379
Q04631 UniProt NPD GO	PFTA_RAT	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.36	-	cyt	0				3FTI	377
P05130 UniProt NPD GO	KPC1_DROME	Protein kinase C, brain isozyme (EC 2.7.11.13) (PKC) (dPKC53E(BR))	0.36	-	nuc	0					679
Q9V574 UniProt NPD GO	L2K1_DROME	Protein lethal(2)k10201 (Wunen region protein B)	0.36	-	nuc	0					221
P83501 UniProt NPD GO	MSTAB_DROME	Protein msta, isoform B	0.36	-	cyt	0					448
Q61074 UniProt NPD GO	PP2CG_MOUSE	Protein phosphatase 2C isoform gamma (EC 3.1.3.16) (PP2C-gamma) (Protein phosphatase magnesium-depen ...	0.36	-	nuc	0	Nucleus	nucleus [IDA]			542
O14235 UniProt NPD GO	POF5_SCHPO	Protein pof5	0.36	-	nuc	0					348
Q5M8Z2 UniProt NPD GO	PREY_XENTR	Protein preY, mitochondrial precursor	0.36	-	mit	0	Mitochondrion (Potential)				122
Q01387 UniProt NPD GO	RAS2_NEUCR	Protein ras-2	0.36	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				229
Q9Y810 UniProt NPD GO	SHY1_SCHPO	Protein shy1 (SURF1-like protein)	0.36	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				290
Q9Y1T5 UniProt NPD GO	SUH_DROSI	Protein suppressor of hairless (Fragment)	0.36	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In imaginal disk, at the onset of differentiatio ...	cytoplasm [ISS] nucleus [ISS]			102
P38191 UniProt NPD GO	MOH1_YEAST	Protein yippee-like MOH1	0.36	-	nuc	0					138
P09178 UniProt NPD GO	ROLB_NICGL	Protein-tyrosine phosphatase rolB (EC 3.1.3.48) (Protein ROL B)	0.36	-	nuc	0					211
Q9WUD9 UniProt NPD GO	SRC_RAT	Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) (p60-Src) (c-Src) (pp60c-src)	0.36	-	nuc	0					535
Q9UN66 UniProt NPD GO	PCDB8_HUMAN	Protocadherin beta 8 precursor (PCDH-beta8) (Protocadherin 3I)	0.36	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606334		801
Q9Y5G4 UniProt NPD GO	PCDG9_HUMAN	Protocadherin gamma A9 precursor (PCDH-gamma-A9)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606296		932
Q5DRB1 UniProt NPD GO	PCDG9_PANTR	Protocadherin gamma A9 precursor (PCDH-gamma-A9)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				932
O95206 UniProt NPD GO	PCDH8_HUMAN	Protocadherin-8 precursor (Arcadlin)	0.36	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS] plasma membrane [TAS]	603580		1070
O18229 UniProt NPD GO	6PGL_CAEEL	Putative 6-phosphogluconolactonase (EC 3.1.1.31) (6PGL)	0.36	-	nuc	0					269
P34649 UniProt NPD GO	YOT3_CAEEL	Putative RIO-type serine/threonine-protein kinase ZK632.3 (EC 2.7.11.1)	0.36	-	nuc	0					510
Q6Z351 UniProt NPD GO	ALDOL_ORYSA	Putative aldehyde oxidase-like protein	0.36	-	cyt	0					1342
Q10074 UniProt NPD GO	YAN9_SCHPO	Putative amino-acid permease C3H1.09c	0.36	+	end	10	Membrane; multi-pass membrane protein (Potential)				656
Q9FKM7 UniProt NPD GO	IAA33_ARATH	Putative auxin-responsive protein IAA33 (Putative indoleacetic acid-induced protein 33)	0.36	-	nuc	0	Nucleus (By similarity)				171
Q9LHS0 UniProt NPD GO	CAP10_ARATH	Putative clathrin assembly protein At5g35200	0.36	-	nuc	0					544
Q9W1U5 UniProt NPD GO	GR59C_DROME	Putative gustatory receptor 59c	0.36	+	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			397
Q9W367 UniProt NPD GO	GR08A_DROME	Putative gustatory receptor 8a	0.36	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			385
Q99MV5 UniProt NPD GO	M10L1_MOUSE	Putative helicase Mov10l1 (EC 3.6.1.-) (Moloney leukemia virus 10-like protein 1) (MOV10-like 1) (Ca ...	0.36	-	nuc	0	Isoform 2: Cytoplasm	intracellular [ISS]			1187
Q9SID3 UniProt NPD GO	GLO2N_ARATH	Putative hydroxyacylglutathione hydrolase 2, mitochondrial precursor (EC 3.1.2.6) (Glyoxalase II) (G ...	0.36	+	mit	0	Mitochondrion (Potential)	mitochondrion [NAS]		1XM8	324
Q60CZ8 UniProt NPD GO	R1A10_SOLDE	Putative late blight resistance protein homolog R1A-10	0.36	-	vac	0	Cytoplasm (By similarity)				1306
Q6L3Z0 UniProt NPD GO	R1B13_SOLDE	Putative late blight resistance protein homolog R1B-13	0.36	-	mit	0	Cytoplasm (By similarity)				1141
P53118 UniProt NPD GO	ROG1_YEAST	Putative lipase ROG1 (EC 3.1.-.-)	0.36	-	cyt	0					685
Q9V6A9 UniProt NPD GO	OR49A_DROME	Putative odorant receptor 49a	0.36	-	mit	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			396
Q9V576 UniProt NPD GO	WUN_DROME	Putative phosphatidate phosphatase (EC 3.1.3.4) (Phosphatidic acid phosphatase type 2) (Protein wune ...	0.36	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			379
O94709 UniProt NPD GO	ODPX_SCHPO	Putative pyruvate dehydrogenase protein X component, mitochondrial precursor (Dihydrolipoamide dehyd ...	0.36	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				456
O64791 UniProt NPD GO	SY124_ARATH	Putative syntaxin-124 (AtSYP124)	0.36	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				303
Q08693 UniProt NPD GO	TRE2_YEAST	Putative zinc metalloprotease TRE2 (EC 3.-.-.-) (Transferrin receptor-like protein 2)	0.36	-	cyt	1	Membrane; single-pass type II membrane protein (Potential)				809

You are viewing entries 35301 to 35350 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.