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
P56092 UniProt NPD GO	EPD1_CANMA	Protein EPD1 precursor (Essential for pseudohyphal development 1)	0.21	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				549
Q05005 UniProt NPD GO	FA23A_RABIT	Protein FAM23A (Brush border protein AdRab-C)	0.21	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				351
Q9H5X1 UniProt NPD GO	FA96A_HUMAN	Protein FAM96A	0.21	-	exc	0					160
Q5F448 UniProt NPD GO	GPR89_CHICK	Protein GPR89A	0.21	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				455
Q14695 UniProt NPD GO	K0087_HUMAN	Protein KIAA0087 (HA1002)	0.21	-	nuc	0					138
Q8NBF6 UniProt NPD GO	K0241_HUMAN	Protein KIAA0241	0.21	-	cyt	0	Membrane; single-pass membrane protein (Potential)				648
Q92567 UniProt NPD GO	K0280_HUMAN	Protein KIAA0280	0.21	-	nuc	0					244
Q8BGZ2 UniProt NPD GO	K0280_MOUSE	Protein KIAA0280	0.21	-	nuc	0					244
O15033 UniProt NPD GO	K0317_HUMAN	Protein KIAA0317	0.21	-	mit	1 *					823
Q28955 UniProt NPD GO	NTAN1_PIG	Protein N-terminal asparagine amidohydrolase (EC 3.5.1.-) (Protein NH2-terminal asparagine deamidase ...	0.21	-	cyt	0	Cytoplasm				309
Q4R4K0 UniProt NPD GO	NDRG2_MACFA	Protein NDRG2	0.21	-	nuc	0	Cytoplasm (By similarity)				357
P47032 UniProt NPD GO	PRY1_YEAST	Protein PRY1 precursor (Pathogen related in Sc 1)	0.21	-	exc	0		endoplasmic reticulum [IDA] extracellular region [IDA] nuclear envelope [IDA] vacuole (sensu Fungi) [IDA]			299
Q9P8V0 UniProt NPD GO	RHO4_ASHGO	Protein RHO4	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				259
P26447 UniProt NPD GO	S10A4_HUMAN	Protein S100-A4 (S100 calcium-binding protein A4) (Metastasin) (Protein Mts1) (Placental calcium-bin ...	0.21	-	nuc	0			114210	1M31	101
P82629 UniProt NPD GO	SCR10_ARATH	Protein SCRL10 precursor	0.21	-	nuc	0					107
Q9H9Y3 UniProt NPD GO	T142B_HUMAN	Protein TMEM142B	0.21	-	mit	0					180
P07259 UniProt NPD GO	PYR1_YEAST	Protein URA1 [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate car ...	0.21	-	cyt	0		cytoplasm [IDA] integral to membrane [IDA] mitochondrion [IDA]			2214
Q8NEX6 UniProt NPD GO	WFD11_HUMAN	Protein WFDC11 precursor	0.21	-	mit	1 *	Secreted protein (Potential)				87
P56705 UniProt NPD GO	WNT4_HUMAN	Protein Wnt-4 precursor	0.21	-	gol	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	603490		351
P12304 UniProt NPD GO	X92_TRYBB	Protein X92	0.21	-	end	1					549
O77286 UniProt NPD GO	U239_DROME	Protein anon-73B1	0.21	+	mit	1 *		integral to membrane [NAS]			87
P54069 UniProt NPD GO	BEM46_SCHPO	Protein bem46	0.21	-	cyt	1 *					299
Q9V3A4 UniProt NPD GO	CSUP_DROME	Protein catecholamines up	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				449
O13811 UniProt NPD GO	PDI2_SCHPO	Protein disulfide-isomerase C17H9.14c precursor (EC 5.3.4.1)	0.21	-	exc	1 *					359
Q62074 UniProt NPD GO	KPCI_MOUSE	Protein kinase C iota type (EC 2.7.11.13) (nPKC-iota) (Atypical protein kinase C-lambda/iota) (aPKC- ...	0.21	-	cyt	0	Endosome (By similarity)	apical part of cell [IDA] cytoplasm [IDA] cytosol [ISS] nucleus [ISS] polarisome [ISS]			586
Q62918 UniProt NPD GO	NELL2_RAT	Protein kinase C-binding protein NELL2 precursor (NEL-like protein 2)	0.21	-	nuc	0	Secreted protein				816
Q02034 UniProt NPD GO	KRUP_PHOPA	Protein krueppel (Fragment)	0.21	-	nuc	0	Nucleus (Probable)				46
P52302 UniProt NPD GO	MBN_DROME	Protein lethal(3)malignant blood neoplasm 1 (Mbn(83))	0.21	-	nuc	1 *	Cytoplasm. Cytoplasm; perinuclear region. Mainly around the nucleus				653
P31383 UniProt NPD GO	2AAA_YEAST	Protein phosphatase PP2A regulatory subunit A (PR65)	0.21	-	nuc	0		bud neck [IDA] bud tip [IDA] cytoplasm [IDA] mating projection tip [IDA] nucleus [IDA] protein phosphatase type 2A complex [TAS] spindle pole body [IDA]			635
Q5DRC7 UniProt NPD GO	PCDB7_PANTR	Protocadherin beta 7 precursor (PCDH-beta7)	0.21	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)				793
Q9Y7Y4 UniProt NPD GO	COX10_SCHPO	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.21	-	cyt	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				387
Q6C0L2 UniProt NPD GO	COX10_YARLI	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.21	-	nuc	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				471
P51175 UniProt NPD GO	PPOX_MOUSE	Protoporphyrinogen oxidase (EC 1.3.3.4) (PPO)	0.21	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	intrinsic to mitochondrial inner membrane [IDA] mitochondrial membrane [ISS]			477
P15285 UniProt NPD GO	PSPB_RABIT	Pulmonary surfactant-associated protein B precursor (SP-B) (6 kDa protein) (Pulmonary surfactant-ass ...	0.21	-	end	0	Secreted protein; extracellular space				370
P50405 UniProt NPD GO	PSPB_MOUSE	Pulmonary surfactant-associated protein B precursor (SP-B) (Pulmonary surfactant-associated proteoli ...	0.21	-	end	0	Secreted protein; extracellular space				377
Q09654 UniProt NPD GO	ARD1_CAEEL	Putative GTP-binding protein ard-1 homolog	0.21	-	cyt	0					539
Q9FHG8 UniProt NPD GO	ATL5N_ARATH	Putative RING-H2 finger protein ATL5N	0.21	-	nuc	1 *					210
P87294 UniProt NPD GO	TCP4_SCHPO	Putative RNA polymerase II transcriptional coactivator	0.21	-	nuc	0	Nucleus (By similarity)				136
Q22295 UniProt NPD GO	UGT50_CAEEL	Putative UDP-glucuronosyltransferase ugt-50 precursor (EC 2.4.1.17) (UDPGT)	0.21	-	end	1 *					525
Q9LQW4 UniProt NPD GO	CAP15_ARATH	Putative clathrin assembly protein At1g14686	0.21	-	cyt	0					339
Q27515 UniProt NPD GO	C13A6_CAEEL	Putative cytochrome P450 CYP13A6 (EC 1.14.-.-)	0.21	-	mit	1 *					518
Q9C2M6 UniProt NPD GO	DOPP_NEUCR	Putative dolichyldiphosphatase (EC 3.6.1.43) (Dolichyl pyrophosphate phosphatase)	0.21	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				282
P42936 UniProt NPD GO	YG4D_YEAST	Putative elongation factor 1 gamma homolog	0.21	-	cyt	0					225
P83293 UniProt NPD GO	GR64A_DROME	Putative gustatory receptor 64a	0.21	-	end	8	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			456
Q9VD74 UniProt NPD GO	GR93C_DROME	Putative gustatory receptor 93c	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			397
Q3EC60 UniProt NPD GO	SUVHA_ARATH	Putative histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH10 (EC 2.1.1.43) (Histone H3-K ...	0.21	-	cyt	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				312
Q7FB56 UniProt NPD GO	MRP15_ARATH	Putative multidrug resistance-associated protein 15 (EC 3.6.3.44) (Glutathione S-conjugate-transport ...	0.21	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				1037
Q9W1P7 UniProt NPD GO	OR59C_DROME	Putative odorant receptor 59c	0.21	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			411
P82985 UniProt NPD GO	OR69B_DROME	Putative odorant receptor 69a, isoform B	0.21	-	cyt	6 *	Membrane; multi-pass membrane protein (Potential)				393
Q9LRM5 UniProt NPD GO	PEL9_ARATH	Putative pectate lyase 9 precursor (EC 4.2.2.2)	0.21	-	exc	1 *					452

You are viewing entries 49951 to 50000 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.