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
Q4PD66 UniProt NPD GO	CCPR2_USTMA	Putative heme-binding peroxidase (EC 1.11.1.-)	0.09	-	pox	0					330
Q7RXY2 UniProt NPD GO	KYNU_NEUCR	Putative kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.09	-	cyt	0	Cytoplasm (By similarity)				468
P82727 UniProt NPD GO	LCR12_ARATH	Putative low-molecular-weight cysteine-rich protein LCR12 precursor	0.09	-	vac	1 *					84
Q21265 UniProt NPD GO	TIMPL_CAEEL	Putative metalloproteinase inhibitor K07C11.5 precursor (TIMP-like protein)	0.09	-	end	0	Secreted protein (Potential)				158
Q9UTG6 UniProt NPD GO	FMT_SCHPO	Putative methionyl-tRNA formyltransferase (EC 2.1.2.9)	0.09	-	cyt	0					340
Q09780 UniProt NPD GO	KIME_SCHPO	Putative mevalonate kinase (EC 2.7.1.36) (MK)	0.09	-	nuc	0	Cytoplasm (Potential)				404
P43617 UniProt NPD GO	YFL5_YEAST	Putative mitochondrial carrier YFR045W	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				285
O60029 UniProt NPD GO	PET8_ASHGO	Putative mitochondrial carrier protein PET8	0.09	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				271
Q8TG23 UniProt NPD GO	MBF1_YARLI	Putative multi-protein-binding factor 1 (Protein YlMBF1)	0.09	-	nuc	0					152
Q9SYI3 UniProt NPD GO	MDR5_ARATH	Putative multidrug resistance protein 5 (P-glycoprotein 5)	0.09	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1230
Q9VNK9 UniProt NPD GO	OR83C_DROME	Putative odorant receptor 83c	0.09	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				397
Q9VHE6 UniProt NPD GO	OR85F_DROME	Putative odorant receptor 85f	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			392
P54185 UniProt NPD GO	OBA5_DROME	Putative odorant-binding protein A5 precursor (Antennal protein 5)	0.09	-	vac	0	Secreted protein (Potential). Secreted in the lumen of the sensilla (Potential)				210
Q04212 UniProt NPD GO	YMT1_YEAST	Putative oxidoreductase YMR041C (EC 1.-.-.-)	0.09	-	nuc	0					335
Q05016 UniProt NPD GO	YM71_YEAST	Putative oxidoreductase YMR226C (EC 1.-.-.-)	0.09	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			267
O70503 UniProt NPD GO	DHBK_MOUSE	Putative steroid dehydrogenase KIK-I (EC 1.1.1.-)	0.09	+	mit	1 *					312
P25381 UniProt NPD GO	YCT5_YEAST	Putative subtilase-type proteinase YCR045C precursor (EC 3.4.21.-)	0.09	-	exc	0					491
P12136 UniProt NPD GO	IF1C_TOBAC	Putative translation initiation factor IF-1, chloroplast	0.09	-	cyt	0	Plastid; chloroplast				96
Q9USN4 UniProt NPD GO	YJA1_SCHPO	Putative transporter C1529.01	0.09	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				462
Q9H493 UniProt NPD GO	CT051_HUMAN	Putative uncharacterized protein C20orf51	0.09	-	nuc	0					79
P38320 UniProt NPD GO	YB74_YEAST	Putative uncharacterized protein YBR224W precursor	0.09	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				171
P43595 UniProt NPD GO	YFI2_YEAST	Putative uncharacterized protein YFR012W precursor	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				202
P53116 UniProt NPD GO	YGO9_YEAST	Putative uncharacterized protein YGL149W precursor	0.09	-	end	1 *					101
P53057 UniProt NPD GO	YGZD_YEAST	Putative uncharacterized protein YGL259W precursor	0.09	-	exc	0					165
Q96GD0 UniProt NPD GO	PLPP_HUMAN	Pyridoxal phosphate phosphatase (EC 3.1.3.74) (PLP phosphatase)	0.09	-	cyt	0					296
O94122 UniProt NPD GO	KPYK_AGABI	Pyruvate kinase (EC 2.7.1.40) (PK)	0.09	-	cyt	0					532
P52489 UniProt NPD GO	KPYK2_YEAST	Pyruvate kinase 2 (EC 2.7.1.40) (PK 2)	0.09	-	mit	0					506
Q9BXR0 UniProt NPD GO	TGT_HUMAN	Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine transglycosylase) (Guanine insertion enz ...	0.09	-	mit	0		ribosome [NAS]	609615		387
Q7SIF9 UniProt NPD GO	PHEB_GRACH	R-phycoerythrin beta chain	0.09	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen. Periphery of the rods of the phycobilisome			1EYX	177
Q8WU17 UniProt NPD GO	RN139_HUMAN	RING finger protein 139 (Translocation in renal carcinoma on chromosome 8)	0.09	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] integral to membrane [TAS]	603046		664
Q8BGI1 UniProt NPD GO	RNF24_MOUSE	RING finger protein 24	0.09	-	mit	1 *					148
Q6FIU7 UniProt NPD GO	REXO3_CANGA	RNA exonuclease 3 (EC 3.1.-.-)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				398
Q920Q6 UniProt NPD GO	MSI2H_MOUSE	RNA-binding protein Musashi homolog 2 (Musashi-2)	0.09	-	cyt	0	Cytoplasm. Associated with polysomes	cytoplasm [IDA] polysome [IDA]			346
P46061 UniProt NPD GO	RGP1_MOUSE	Ran GTPase-activating protein 1	0.09	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] perinuclear region [IDA]		1KPS	589
P41912 UniProt NPD GO	ERFD_YEAST	Ras modification protein ERF4 (Hyperactive Ras suppressor protein 5)	0.09	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	extrinsic to endoplasmic reticulum membrane [IDA] palmitoyltransferase complex [IPI]			237
Q01890 UniProt NPD GO	YPT1_PHYIN	Ras-like GTP-binding protein YPT1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
P83832 UniProt NPD GO	RAS1_DROMA	Ras-like protein 1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				189
P08646 UniProt NPD GO	RAS1_DROME	Ras-like protein 1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				189
P83831 UniProt NPD GO	RAS1_DROSI	Ras-like protein 1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				189
P51539 UniProt NPD GO	RAS1_HYDMA	Ras-like protein RAS1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
P19892 UniProt NPD GO	ARA1_ARATH	Ras-related protein ARA-1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				218
P90726 UniProt NPD GO	RAB18_CAEBR	Ras-related protein Rab-18	0.09	-	cyt	0					202
Q8MXS1 UniProt NPD GO	RAB18_CAEEL	Ras-related protein Rab-18	0.09	-	cyt	0					203
Q99KL7 UniProt NPD GO	RAB28_MOUSE	Ras-related protein Rab-28	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				221
Q64008 UniProt NPD GO	RAB34_MOUSE	Ras-related protein Rab-34 (Rab-39) (Ras-related protein Rah) (Ras-related homolog)	0.09	-	cyt	0	Cytoplasm. Golgi apparatus. Associates with the Golgi complex	early endosome [IDA] ruffle [IDA]			259
Q91ZR1 UniProt NPD GO	RAB4B_MOUSE	Ras-related protein Rab-4B	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P51146 UniProt NPD GO	RAB4B_RAT	Ras-related protein Rab-4B	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
Q40193 UniProt NPD GO	RB11C_LOTJA	Ras-related protein Rab11C	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
P36860 UniProt NPD GO	RALB_RAT	Ras-related protein Ral-B	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
P18613 UniProt NPD GO	RAP1_DICDI	Ras-related protein Rap-1	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				186

You are viewing entries 66951 to 67000 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.