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
P00523 UniProt NPD GO	SRC_CHICK	Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) (p60-Src) (c-Src) (pp60c-src)	0.46	-	nuc	0				2PTK	532
P07949 UniProt NPD GO	RET_HUMAN	Proto-oncogene tyrosine-protein kinase receptor ret precursor (EC 2.7.10.1) (C-ret)	0.46	-	end	1 *	Membrane; single-pass type I membrane protein		209880		1114
Q5DRC2 UniProt NPD GO	PCDG1_PANTR	Protocadherin gamma A1 precursor (PCDH-gamma-A1)	0.46	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				931
O76454 UniProt NPD GO	PHS_DROME	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.46	-	mit	0					192
Q9SMT4 UniProt NPD GO	RL132_ARATH	Putative 60S ribosomal protein L13-2	0.46	-	nuc	0					206
O19892 UniProt NPD GO	YCF30_CYACA	Putative HTH-type transcriptional regulator ycf30	0.46	-	nuc	0	Plastid; chloroplast				317
Q9LNB9 UniProt NPD GO	LBD2_ARATH	Putative LOB domain-containing protein 2	0.46	-	mit	0					205
Q9FGK3 UniProt NPD GO	MO25N_ARATH	Putative MO25-like protein At5g47540	0.46	-	nuc	0					343
Q9C7I1 UniProt NPD GO	ATL1H_ARATH	Putative RING-H2 finger protein ATL1H precursor	0.46	-	end	2 *					327
Q9ZV53 UniProt NPD GO	ATL2C_ARATH	Putative RING-H2 finger protein ATL2C	0.46	-	nuc	1 *					423
Q12424 UniProt NPD GO	YD206_YEAST	Putative cation exchanger YDL206W precursor	0.46	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				762
Q9SCN8 UniProt NPD GO	CD48D_ARATH	Putative cell division control protein 48 homolog D (AtCDC48d) (Transitional endoplasmic reticulum A ...	0.46	-	cyt	0	Nucleus (By similarity). Phragmoplast (By similarity). Primarily localized to the nucleus and, durin ...				815
Q9SH22 UniProt NPD GO	DRL20_ARATH	Putative disease resistance protein At1g63360	0.46	-	cyt	0					884
P33543 UniProt NPD GO	TMKL1_ARATH	Putative kinase-like protein TMKL1 precursor	0.46	-	end	1 *	Membrane; single-pass type I membrane protein				674
Q5A4N0 UniProt NPD GO	ATG15_CANAL	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.46	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				597
Q9M149 UniProt NPD GO	PI5KB_ARATH	Putative phosphatidylinositol-4-phosphate 5-kinase 11 (EC 2.7.1.68) (AtPIP5K11) (1-phosphatidylinosi ...	0.46	-	nuc	0					401
Q22031 UniProt NPD GO	RRMJ2_CAEEL	Putative ribosomal RNA methyltransferase R74.7 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase) ...	0.46	-	nuc	0					337
P91409 UniProt NPD GO	STX4_CAEEL	Putative syntaxin-4	0.46	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	integral to membrane [ISS]			287
O22779 UniProt NPD GO	TRXL7_ARATH	Putative thioredoxin-like 7, chloroplast precursor	0.46	-	nuc	0	Plastid; chloroplast (Potential)				273
P53977 UniProt NPD GO	YNB7_YEAST	Putative uncharacterized protein YNL017C	0.46	-	nuc	0					112
P38075 UniProt NPD GO	PDX3_YEAST	Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx)	0.46	-	cyt	0				1CI0	228
P54644 UniProt NPD GO	KRAC_DICDI	RAC-family serine/threonine-protein kinase homolog (EC 2.7.11.1)	0.46	-	cyt	0					444
Q96EQ8 UniProt NPD GO	RN125_HUMAN	RING finger protein 125 (EC 6.3.2.-) (T-cell RING activation protein 1) (TRAC-1)	0.46	-	nuc	0					231
Q6DIP3 UniProt NPD GO	RN126_XENTR	RING finger protein 126	0.46	-	nuc	0					311
Q7T0Q3 UniProt NPD GO	R126A_XENLA	RING finger protein 126-A	0.46	-	nuc	0					312
Q6IRP0 UniProt NPD GO	R126B_XENLA	RING finger protein 126-B	0.46	-	nuc	0					312
Q75B51 UniProt NPD GO	TFB2_ASHGO	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.46	-	cyt	0	Nucleus (By similarity)				514
Q6CLR2 UniProt NPD GO	TFB2_KLULA	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.46	-	cyt	0	Nucleus (By similarity)				496
Q62921 UniProt NPD GO	UB7I3_RAT	RanBP-type and C3HC4-type zinc finger-containing protein 1 (Ubiquitin-conjugating enzyme 7-interacti ...	0.46	-	nuc	0					498
Q9WUB0 UniProt NPD GO	UB7I3_MOUSE	RanBP-type and C3HC4-type zinc finger-containing protein 1 (Ubiquitin-conjugating enzyme 7-interacti ...	0.46	-	nuc	0					498
O95398 UniProt NPD GO	RPGF3_HUMAN	Rap guanine nucleotide exchange factor 3 (cAMP-regulated guanine nucleotide exchange factor I) (cAMP ...	0.46	-	mit	0	Intracytoplasmic membrane	membrane fraction [TAS]	606057		881
Q02833 UniProt NPD GO	RASF7_HUMAN	Ras association domain-containing protein 7 (HRAS1-related cluster protein 1)	0.46	+	nuc	0		nucleus [NAS]	143023		373
P24498 UniProt NPD GO	RAS_GEOCY	Ras-like protein	0.46	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				209
Q5VZM2 UniProt NPD GO	RRAGB_HUMAN	Ras-related GTP-binding protein B (Rag B) (RagB)	0.46	-	cyt	0	Cytoplasm				374
Q5RB22 UniProt NPD GO	ERBB3_PONPY	Receptor tyrosine-protein kinase erbB-3 precursor (EC 2.7.10.1)	0.46	+	exc	1	Membrane; single-pass type I membrane protein (By similarity)				1342
Q5QGU6 UniProt NPD GO	RTP3_MOUSE	Receptor-transporting protein 3 (Transmembrane protein 7)	0.46	-	cyt	0	Membrane; single-pass type III membrane protein (Potential)				474
P23469 UniProt NPD GO	PTPRE_HUMAN	Receptor-type tyrosine-protein phosphatase epsilon precursor (EC 3.1.3.48) (Protein-tyrosine phospha ...	0.46	-	end	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Cytoplasm		600926		700
O14921 UniProt NPD GO	RGS13_HUMAN	Regulator of G-protein signaling 13 (RGS13)	0.46	-	nuc	0			607190		159
Q8K443 UniProt NPD GO	RGS13_MOUSE	Regulator of G-protein signaling 13 (RGS13)	0.46	-	nuc	0		cytosol [IDA] nucleus [IDA] plasma membrane [IDA]			158
Q9QZB1 UniProt NPD GO	RGS20_MOUSE	Regulator of G-protein signaling 20 (RGS20) (Regulator of G-protein signaling Z1)	0.46	-	nuc	0	Membrane; lipid-anchor (Potential)	Golgi apparatus [TAS]			239
P11491 UniProt NPD GO	PPB_YEAST	Repressible alkaline phosphatase precursor (EC 3.1.3.1)	0.46	-	mit	1 *	Vacuole. Lysosome-like vacuoles	vacuolar membrane (sensu Fungi) [IDA]			566
Q9N0E3 UniProt NPD GO	RTN4R_MACFA	Reticulon-4 receptor precursor (Nogo receptor) (NgR) (Nogo-66 receptor)	0.46	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				473
Q86UN3 UniProt NPD GO	R4RL2_HUMAN	Reticulon-4 receptor-like 2 precursor (Nogo-66 receptor homolog 1) (Nogo-66 receptor-related protein ...	0.46	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Localized to the surface of neurons, including axons	anchored to plasma membrane [IDA]			420
Q80WD1 UniProt NPD GO	R4RL2_RAT	Reticulon-4 receptor-like 2 precursor (Nogo-66 receptor homolog 1) (Nogo-66 receptor-related protein ...	0.46	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential). Localized to the surface of neurons, including ...	anchored to plasma membrane [ISS] external side of plasma membrane [IDA] lipid raft [IDA]			420
Q90417 UniProt NPD GO	RXRD_BRARE	Retinoic acid receptor RXR-delta (Retinoid X receptor delta)	0.46	+	nuc	0	Nucleus	nucleus [NAS]			422
Q9Y5P3 UniProt NPD GO	RAI2_HUMAN	Retinoic acid-induced protein 2	0.46	-	nuc	0			300217		530
Q8TCX5 UniProt NPD GO	RHPN1_HUMAN	Rhophilin-1 (GTP-Rho-binding protein 1)	0.46	-	nuc	0			601031		695
P40571 UniProt NPD GO	RPR2_YEAST	Ribonuclease P protein subunit RPR2 (EC 3.1.26.5)	0.46	-	nuc	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA]			144
Q8SR37 UniProt NPD GO	RIR1_ENCCU	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase)	0.46	-	cyt	0					768
Q75ET5 UniProt NPD GO	RLP7_ASHGO	Ribosome biogenesis protein RLP7	0.46	-	mit	0	Nucleus; nucleolus (By similarity)				293

You are viewing entries 27901 to 27950 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.