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
Q10464 UniProt NPD GO	PUIB_WHEAT	Puroindoline-B precursor	0.15	-	exc	0					148
P87228 UniProt NPD GO	SERA_SCHPO	Putative D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH)	0.15	-	cyt	0					466
Q9LT45 UniProt NPD GO	GAT18_ARATH	Putative GATA transcription factor 18	0.15	-	nuc	0	Nucleus (Probable)				208
Q9FLC6 UniProt NPD GO	ATL5B_ARATH	Putative RING-H2 finger protein ATL5B precursor	0.15	-	mit	1 *					176
Q09295 UniProt NPD GO	YQO4_CAEEL	Putative RNA-binding protein EEED8.4	0.15	-	cyt	0					237
P39533 UniProt NPD GO	ACON2_YEAST	Putative aconitase YJL200C (EC 4.2.1.3)	0.15	-	nuc	0		mitochondrion [IDA]			789
O42887 UniProt NPD GO	SPEB2_SCHPO	Putative agmatinase 2 precursor (EC 3.5.3.11) (Agmatine ureohydrolase) (AUH)	0.15	-	exc	0					413
P42884 UniProt NPD GO	AAD14_YEAST	Putative aryl-alcohol dehydrogenase AAD14 (EC 1.1.1.-)	0.15	-	cyt	0					376
O14073 UniProt NPD GO	YEA8_SCHPO	Putative dipeptidyl aminopeptidase C2E11.08 (EC 3.4.14.-)	0.15	-	cyt	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein (By similarity). Lysosome-like vacu ...				793
Q9LW09 UniProt NPD GO	DRL22_ARATH	Putative disease resistance protein At3g15700	0.15	-	cyt	0					375
P45699 UniProt NPD GO	GUNK_FUSOX	Putative endoglucanase type K precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase)	0.15	-	exc	0					376
Q9M9U0 UniProt NPD GO	GT4_ARATH	Putative glycosyltransferase 4 (EC 2.4.-.-) (AtGT4)	0.15	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				513
Q9VPT1 UniProt NPD GO	GR21A_DROME	Putative gustatory receptor 21a	0.15	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			447
P83295 UniProt NPD GO	GR64C_DROME	Putative gustatory receptor 64c	0.15	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			419
Q59X94 UniProt NPD GO	CCPR2_CANAL	Putative heme-binding peroxidase (EC 1.11.1.-)	0.15	-	mit	0					291
Q39366 UniProt NPD GO	LGUL_BRAOG	Putative lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (G ...	0.15	+	cyt	0					282
Q8S8H9 UniProt NPD GO	LCR10_ARATH	Putative low-molecular-weight cysteine-rich protein LCR10 precursor	0.15	-	exc	1 *					81
P82733 UniProt NPD GO	LCR19_ARATH	Putative low-molecular-weight cysteine-rich protein LCR19 precursor	0.15	-	nuc	0					126
P82760 UniProt NPD GO	LCR45_ARATH	Putative low-molecular-weight cysteine-rich protein LCR45 precursor	0.15	-	exc	0					82
Q09461 UniProt NPD GO	YQ51_CAEEL	Putative mitochondrial carrier C16C10.1	0.15	-	end	4	Membrane; multi-pass membrane protein (Potential)				360
Q9W5G6 UniProt NPD GO	OR1A_DROME	Putative odorant receptor 1a	0.15	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			392
Q9V9I2 UniProt NPD GO	OR42A_DROME	Putative odorant receptor 42a	0.15	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			406
O96669 UniProt NPD GO	SCK_MESTA	Putative potassium channel blocker (Fragment)	0.15	-	nuc	0	Secreted protein (By similarity)				45
Q17374 UniProt NPD GO	SUP10_CAEEL	Putative potassium channel regulatory protein sup-10 precursor (Suppressor of unc-93 protein 10)	0.15	-	end	2 *	Membrane; single-pass type I membrane protein (Potential). Associated with dense bodies	integral to plasma membrane [NAS]			332
P53825 UniProt NPD GO	YN64_YEAST	Putative uncharacterized protein YNL324W	0.15	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				131
P53820 UniProt NPD GO	YN78_YEAST	Putative uncharacterized protein YNL338W	0.15	-	nuc	0					52
Q90673 UniProt NPD GO	PX19_CHICK	Px19-like protein	0.15	-	mit	0					215
O17732 UniProt NPD GO	PYC1_CAEEL	Pyruvate carboxylase 1 (EC 6.4.1.1) (Pyruvic carboxylase 1) (PCB 1)	0.15	-	mit	0	Cytoplasm (By similarity)				1175
P52873 UniProt NPD GO	PYC_RAT	Pyruvate carboxylase, mitochondrial precursor (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix				1178
Q39735 UniProt NPD GO	PPDK_FLABI	Pyruvate, phosphate dikinase, chloroplast precursor (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase) ...	0.15	-	cyt	0	Plastid; chloroplast				953
P31750 UniProt NPD GO	AKT1_MOUSE	RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-alpha) (AKT1 kinase) (Protein kinase ...	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus after activation by integrin-linked prot ...	cytoplasm [IDA] lamellipodium [IDA] spindle [IDA]			480
Q5ZIR9 UniProt NPD GO	RN185_CHICK	RING finger protein 185	0.15	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				194
Q9HDW3 UniProt NPD GO	TFB5_SCHPO	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.15	-	cyt	0	Nucleus (By similarity)				68
O93614 UniProt NPD GO	GDS1A_XENLA	Rap1 GTPase-GDP dissociation stimulator 1-A (RalB-binding protein-A) (Rap1gds1-A protein) (smgGDS-A) ...	0.15	-	nuc	0					607
Q40723 UniProt NPD GO	RGP2_ORYSA	Ras-related protein RGP2 (GTP-binding regulatory protein RGP2)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q9CQD1 UniProt NPD GO	RAB5A_MOUSE	Ras-related protein Rab-5A	0.15	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...	early endosome [IDA] endocytic vesicle [IDA] lipid raft [IDA] plasma membrane [IDA] ruffle [IDA]			215
P18067 UniProt NPD GO	RAB7_CANFA	Ras-related protein Rab-7	0.15	-	cyt	0	Endosome; late endosome. Lysosome (By similarity). Phagosome (By similarity). Found on late lysosome ...				207
O14966 UniProt NPD GO	RAB7L_HUMAN	Ras-related protein Rab-7L1 (Rab-7-like protein 1)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		603949		203
Q96AH8 UniProt NPD GO	RAB7B_HUMAN	Ras-related protein Rab-7b	0.15	-	cyt	0	Lysosome. Associated with lysosomal organelles				199
P36409 UniProt NPD GO	RAB2_DICDI	Ras-related protein Rab2 (Fragment)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
P31022 UniProt NPD GO	RAB7_PEA	Ras-related protein Rab7	0.15	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
Q9HEH1 UniProt NPD GO	RENT1_NEUCR	Regulator of nonsense transcripts 1 homolog	0.15	-	nuc	0	Cytoplasm (Potential)				1093
Q9BQ08 UniProt NPD GO	RSNB_HUMAN	Resistin-like beta precursor (RELMbeta) (Cysteine-rich secreted protein FIZZ2) (Colon and small inte ...	0.15	-	exc	0	Secreted protein		605645		111
Q8BH97 UniProt NPD GO	RCN3_MOUSE	Reticulocalbin-3 precursor	0.15	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				328
Q9EQQ8 UniProt NPD GO	CNRG_CAVPO	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GMP ...	0.15	-	cyt	0					87
Q9UHP6 UniProt NPD GO	RTDR1_HUMAN	Rhabdoid tumor deletion region protein 1	0.15	-	cyt	0			605663		348
P31356 UniProt NPD GO	OPSD_TODPA	Rhodopsin	0.15	-	end	6 *	Membrane; multi-pass membrane protein				447
P53259 UniProt NPD GO	PCP1_YEAST	Rhomboid protein 1, mitochondrial precursor (EC 3.4.21.105) (Processing of cytochrome c peroxidase p ...	0.15	-	mit	6	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [TAS]			346
P42815 UniProt NPD GO	RNS3_ARATH	Ribonuclease 3 precursor (EC 3.1.27.1)	0.15	-	vac	0					222
Q9TL10 UniProt NPD GO	RNE_NEPOL	Ribonuclease E homolog (EC 3.1.4.-) (RNase E)	0.15	-	cyt	0	Plastid; chloroplast				375

You are viewing entries 57551 to 57600 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.