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
Q04048 UniProt NPD GO	SYF1_YEAST	Pre-mRNA-splicing factor SYF1 (Synthetic lethal with CDC40 protein 1) (PRP19-associated complex prot ...	0.62	-	nuc	0	Nucleus	spliceosome complex [IDA]			859
P93768 UniProt NPD GO	PSD3_TOBAC	Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Nuclear antigen ...	0.62	-	nuc	0	Nucleus				488
Q9LNU4 UniProt NPD GO	PSD31_ARATH	Probable 26S proteasome non-ATPase regulatory subunit 3a (26S proteasome subunit S3-a)	0.62	-	nuc	0					488
Q9HDV5 UniProt NPD GO	RM02_SCHPO	Probable 60S ribosomal protein L2, mitochondrial precursor	0.62	-	mit	0	Mitochondrion (By similarity)				153
Q924Y8 UniProt NPD GO	GP149_RAT	Probable G-protein coupled receptor 149 (Induced early in differentiating astrocytes gene protein)	0.62	-	end	7 *	Membrane; multi-pass membrane protein				730
Q03210 UniProt NPD GO	NGL3_YEAST	Probable RNA exonuclease NGL3 (EC 3.1.-.-)	0.62	-	nuc	0					505
Q93WY4 UniProt NPD GO	WRK12_ARATH	Probable WRKY transcription factor 12 (WRKY DNA-binding protein 12)	0.62	+	nuc	0	Nucleus (Probable)				218
Q9SHB5 UniProt NPD GO	WRK55_ARATH	Probable WRKY transcription factor 55 (WRKY DNA-binding protein 55)	0.62	-	nuc	0	Nucleus (Probable)				292
Q8VWV6 UniProt NPD GO	WRK61_ARATH	Probable WRKY transcription factor 61 (WRKY DNA-binding protein 61)	0.62	-	nuc	0	Nucleus (Potential)				480
Q9LXG8 UniProt NPD GO	WRK72_ARATH	Probable WRKY transcription factor 72 (WRKY DNA-binding protein 72)	0.62	-	nuc	0	Nucleus (Probable)				548
Q8GWD2 UniProt NPD GO	CNG12_ARATH	Probable cyclic nucleotide-gated ion channel 12 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.62	+	end	5 *	Cell membrane; multi-pass membrane protein (Potential)				649
Q9VMS7 UniProt NPD GO	C4AC3_DROME	Probable cytochrome P450 4ac3 (EC 1.14.-.-) (CYPIVAC3)	0.62	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				509
Q9URX8 UniProt NPD GO	NG06_SCHPO	Probable nucleoporin C890.06	0.62	-	mit	0	Cytoplasm. Nucleus; nucleoplasm; nuclear rim				1315
Q05534 UniProt NPD GO	PHOG_EMENI	Probable phosphate-non-repressible acid phosphatase precursor (EC 3.1.3.2)	0.62	-	nuc	0					330
P39524 UniProt NPD GO	ATC3_YEAST	Probable phospholipid-transporting ATPase DRS2 (EC 3.6.3.1)	0.62	-	end	9	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein	Golgi membrane [IDA] Golgi trans face [IDA] plasma membrane [TAS] trans-Golgi network transport vesicle [IDA]			1355
Q6ZBH9 UniProt NPD GO	NCKP1_ORYSA	Probable protein NAP1 (Nck-associated protein 1) (P125Nap1) (NAP of plants)	0.62	-	nuc	0					1359
Q86B05 UniProt NPD GO	RLP24_DICDI	Probable ribosome biogenesis protein RLP24	0.62	-	nuc	0	Nucleus; nucleolus (By similarity)				164
P36005 UniProt NPD GO	KKQ1_YEAST	Probable serine/threonine-protein kinase YKL161C (EC 2.7.11.1)	0.62	-	cyt	0					433
P56287 UniProt NPD GO	EI2BE_SCHPO	Probable translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subuni ...	0.62	-	nuc	0					678
Q9TXV7 UniProt NPD GO	TYDP_CAEEL	Probable tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) (Tyr-DNA phosphodiesterase)	0.62	-	mit	0	Nucleus (Probable)				451
Q5RBP8 UniProt NPD GO	PROP_PONPY	Properdin precursor (Factor P)	0.62	-	exc	0	Secreted protein				469
Q8GW20 UniProt NPD GO	Y5390_ARATH	Protein At5g03900 precursor	0.62	-	end	3	Membrane; multi-pass membrane protein (Potential)				523
Q5XI53 UniProt NPD GO	CJ046_RAT	Protein C10orf46 homolog	0.62	-	nuc	0					347
Q9P7L2 UniProt NPD GO	YOSB_SCHPO	Protein C21C3.11 in chromosome II	0.62	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			425
Q9NXL9 UniProt NPD GO	CF061_HUMAN	Protein C6orf61	0.62	-	nuc	0					136
Q9BE21 UniProt NPD GO	CI090_MACFA	Protein C9orf90 homolog	0.62	-	nuc	0					327
Q6PFD7 UniProt NPD GO	CI090_MOUSE	Protein C9orf90 homolog	0.62	-	nuc	0					327
P25603 UniProt NPD GO	CWH36_YEAST	Protein CWH36	0.62	+	nuc	1					130
Q9ULQ0 UniProt NPD GO	FA40B_HUMAN	Protein FAM40B	0.62	-	cyt	0					834
Q5ZJV7 UniProt NPD GO	FA60A_CHICK	Protein FAM60A	0.62	+	nuc	0					222
Q5R679 UniProt NPD GO	FA98A_PONPY	Protein FAM98A	0.62	+	cyt	0					518
P43535 UniProt NPD GO	GCN20_YEAST	Protein GCN20	0.62	-	nuc	0		cytosol [IPI] cytosolic ribosome (sensu Eukaryota) [IDA]			752
Q6R2V0 UniProt NPD GO	HSN2_PIG	Protein HSN2 precursor	0.62	-	nuc	0	Secreted protein (Potential)				433
Q5VV43 UniProt NPD GO	K0319_HUMAN	Protein KIAA0319 precursor	0.62	-	end	1	Membrane; single-pass type I membrane protein (Potential)		609269		1072
O15091 UniProt NPD GO	K0391_HUMAN	Protein KIAA0391	0.62	-	cyt	0			609947		567
Q6ZPU9 UniProt NPD GO	K1279_MOUSE	Protein KIAA1279	0.62	-	cyt	0					617
Q80U72 UniProt NPD GO	LAP4_MOUSE	Protein LAP4 (Protein scribble homolog)	0.62	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Localized to cell ...				1612
Q872S3 UniProt NPD GO	OS9_NEUCR	Protein OS-9 homolog precursor	0.62	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				590
P40960 UniProt NPD GO	PAC11_YEAST	Protein PAC11	0.62	-	nuc	0		cytoplasmic dynein complex [TAS] cytoplasmic microtubule [IDA]			533
Q6FK07 UniProt NPD GO	PET20_CANGA	Protein PET20, mitochondrial precursor	0.62	-	mit	0	Mitochondrion (By similarity)				267
P40463 UniProt NPD GO	VHS2_YEAST	Protein VHS2 (Viable in a HAL3 SIT4 background protein 2)	0.62	-	nuc	0	Cytoplasm	cytoplasm [IDA]			436
Q01617 UniProt NPD GO	CPO_DROME	Protein couch potato	0.62	-	exc	0	Nucleus	nucleus [IDA]			738
Q86UW9 UniProt NPD GO	DTX2_HUMAN	Protein deltex-2 (Deltex-2) (Deltex2) (hDTX2)	0.62	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Partially				622
P23023 UniProt NPD GO	DSX_DROME	Protein doublesex	0.62	-	nuc	0				1ZV1	549
Q61645 UniProt NPD GO	HAIR_MOUSE	Protein hairless	0.62	-	nuc	0	Nucleus				1182
Q03345 UniProt NPD GO	LIN3_CAEEL	Protein lin-3 precursor (Abnormal cell lineage protein 3) (Lethal protein 94)	0.62	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			438
Q10325 UniProt NPD GO	MST2_SCHPO	Protein mst2	0.62	-	nuc	0		nuclear chromatin [IDA]			407
P23803 UniProt NPD GO	ODD_DROME	Protein odd-skipped	0.62	-	nuc	0	Nucleus (Probable)	nucleus [IC]			392
Q16821 UniProt NPD GO	PPR3A_HUMAN	Protein phosphatase 1 regulatory subunit 3A (Protein phosphatase 1 glycogen-associated regulatory su ...	0.62	-	nuc	1	Membrane; single-pass membrane protein (By similarity)		600917		1122
P49412 UniProt NPD GO	PRIB_LENED	Protein priB	0.62	-	nuc	0	Nucleus (By similarity)				565

You are viewing entries 18101 to 18150 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.