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
P38969 UniProt NPD GO	PNT1_YEAST	Pentamidine resistance factor, mitochondrial precursor	0.30	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)	mitochondrial inner membrane [IDA]			423
O55103 UniProt NPD GO	PRAX_MOUSE	Periaxin	0.30	-	nuc	0	Nucleus. Isoform 1: Cell membrane. Isoform 1 is associated with plasma membrane during myelination. ...	cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			1391
P91341 UniProt NPD GO	PWP2_CAEEL	Periodic tryptophan protein 2 homolog	0.30	-	cyt	0					910
Q9LDN9 UniProt NPD GO	PER37_ARATH	Peroxidase 37 precursor (EC 1.11.1.7) (Atperox P37) (ATP38)	0.30	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				346
Q8C0L6 UniProt NPD GO	PAOX_MOUSE	Peroxisomal N1-acetyl-spermine/spermidine oxidase (EC 1.5.3.11) (Polyamine oxidase)	0.30	-	cyt	0	Peroxisome (By similarity). Cytoplasm (By similarity)				503
P15202 UniProt NPD GO	CATA_YEAST	Peroxisomal catalase A (EC 1.11.1.6)	0.30	-	pox	0	Peroxisome	mitochondrion [IDA]		1A4E	515
P12807 UniProt NPD GO	AMO_PICAN	Peroxisomal copper amine oxidase (EC 1.4.3.6) (Methylamine oxidase)	0.30	-	mit	0	Peroxisome			1EKM	692
Q6P6M5 UniProt NPD GO	PX11C_MOUSE	Peroxisomal membrane protein 11C (Peroxin-11C) (Peroxisomal biogenesis factor 11C) (PEX11gamma) (Pex ...	0.30	-	mit	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				241
P21245 UniProt NPD GO	PM47A_CANBO	Peroxisomal membrane protein PMP47A	0.30	-	end	4 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein				423
P79371 UniProt NPD GO	SOX_RABIT	Peroxisomal sarcosine oxidase (EC 1.5.3.1) (PSO) (L-pipecolate oxidase) (EC 1.5.3.7) (L-pipecolic ac ...	0.30	-	mit	1 *	Peroxisome				390
Q752X0 UniProt NPD GO	PEX5_ASHGO	Peroxisomal targeting signal receptor (Peroxin-5) (PTS1 receptor)	0.30	-	cyt	0	Cytoplasm (By similarity). Peroxisome; peroxisomal membrane; peripheral membrane protein (By similar ...				569
Q8HYL6 UniProt NPD GO	PPARA_PHACI	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.30	+	nuc	0	Nucleus (By similarity)				468
Q9R0I8 UniProt NPD GO	PI52A_RAT	Phosphatidylinositol-4-phosphate 5-kinase type-2 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.30	-	mit	0					406
O93233 UniProt NPD GO	PLIB_AGKBL	Phospholipase A2 inhibitor subunit B precursor (PLI-B)	0.30	+	exc	0					331
Q41142 UniProt NPD GO	PLDA1_RICCO	Phospholipase D alpha 1 precursor (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine- ...	0.30	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole. Endoplasm ...				808
O15067 UniProt NPD GO	PUR4_HUMAN	Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) (FGAM synthase) (FGAMS) (Formylglycinamide r ...	0.30	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]	602133		1338
Q76L34 UniProt NPD GO	PCYAA_ASTLO	Photoactivated adenylate cyclase subunit alpha (EC 4.6.1.1) (Photoactivated adenylyl cyclase subunit ...	0.30	-	cyt	0	Flagellum	flagellum [IDA]			1019
P20454 UniProt NPD GO	YCF4_HORVU	Photosystem I assembly protein ycf4 (Fragment)	0.30	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				130
P42498 UniProt NPD GO	PHYE_ARATH	Phytochrome E	0.30	-	cyt	0					1112
P53797 UniProt NPD GO	PSY_NARPS	Phytoene synthase, chloroplast precursor (EC 2.5.1.-)	0.30	-	mit	1	Plastid; chloroplast				423
Q9DAZ2 UniProt NPD GO	PRLPK_MOUSE	Placental prolactin-like protein K precursor (PRL-like protein K) (PLP-K)	0.30	-	exc	0	Secreted protein (By similarity)				228
P49380 UniProt NPD GO	PMA1_KLULA	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.30	+	end	8	Cell membrane; multi-pass membrane protein				899
Q9TTY5 UniProt NPD GO	PTAFR_BOVIN	Platelet-activating factor receptor (PAF-R) (PAFr)	0.30	-	end	7 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [IDA]			342
P21259 UniProt NPD GO	PRFA_POLPE	Pol-RFamide neuropeptides precursor [Contains: Pol-RFamide-II; Pol-RFamide-I; Neuropeptide]	0.30	-	exc	0	Secreted protein				287
P29675 UniProt NPD GO	SF3_HELAN	Pollen-specific protein SF3	0.30	-	nuc	0					219
Q15366 UniProt NPD GO	PCBP2_HUMAN	Poly(rC)-binding protein 2 (Alpha-CP2) (hnRNP-E2)	0.30	-	nuc	0	Nucleus. Cytoplasm. Loosely bound in the nucleus. May shuttle between the nucleus and the cytoplasm	cytoplasm [NAS] nucleus [NAS]	601210	2AXY	365
Q9M5J9 UniProt NPD GO	PGIP1_ARATH	Polygalacturonase inhibitor 1 precursor (Polygalacturonase-inhibiting protein) (PGIP-1)	0.30	-	exc	0	Cell wall; peripheral membrane protein				330
O54724 UniProt NPD GO	PTRF_MOUSE	Polymerase I and transcript release factor	0.30	-	nuc	0	Cell membrane; caveola (By similarity). Found at the surface of the caveolae. Cell membrane (By simi ...	nucleus [IDA]			392
O08912 UniProt NPD GO	GALT1_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.30	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...			1XHB	559
O94048 UniProt NPD GO	HEM3_CANAL	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.30	-	nuc	0					340
Q6BM23 UniProt NPD GO	HEM3_DEBHA	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.30	-	nuc	0					361
Q9NPC2 UniProt NPD GO	KCNK9_HUMAN	Potassium channel subfamily K member 9 (Acid-sensitive potassium channel protein TASK-3) (TWIK-relat ...	0.30	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [NAS]	605874		374
P29187 UniProt NPD GO	TXSHK_STOHE	Potassium channel toxin ShK	0.30	-	mit	0	Secreted protein. Found in nematocyst			1ROO	35
P16388 UniProt NPD GO	KCNA1_MOUSE	Potassium voltage-gated channel subfamily A member 1 (Voltage-gated potassium channel subunit Kv1.1) ...	0.30	-	end	4	Membrane; multi-pass membrane protein				495
P63160 UniProt NPD GO	KCNE2_CAVPO	Potassium voltage-gated channel subfamily E member 2 (Minimum potassium ion channel-related peptide ...	0.30	-	nuc	1 *	Membrane; single-pass type I membrane protein				123
P63161 UniProt NPD GO	KCNE2_RAT	Potassium voltage-gated channel subfamily E member 2 (Minimum potassium ion channel-related peptide ...	0.30	-	nuc	1 *	Membrane; single-pass type I membrane protein				123
Q9QYU3 UniProt NPD GO	KCNG2_RAT	Potassium voltage-gated channel subfamily G member 2 (Voltage-gated potassium channel subunit Kv6.2) ...	0.30	-	end	5	Membrane; multi-pass membrane protein				480
P09626 UniProt NPD GO	ATP4A_RAT	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.30	-	end	8	Membrane; multi-pass membrane protein				1032
Q9TV52 UniProt NPD GO	AT12A_RABIT	Potassium-transporting ATPase alpha chain 2 (EC 3.6.3.10) (Proton pump) (Non-gastric H(+)/K(+) ATPas ...	0.30	+	end	8	Membrane; multi-pass membrane protein				1094
Q5ZMA2 UniProt NPD GO	PRP19_CHICK	Pre-mRNA-splicing factor 19 (PRP19/PSO4 homolog)	0.30	-	cyt	0	Nucleus (By similarity). Nucleoplasmic in interphase cells. Irregularly distributed in anaphase cell ...				505
Q07350 UniProt NPD GO	PRP11_YEAST	Pre-mRNA-splicing factor PRP11	0.30	-	nuc	0	Nucleus (By similarity)	snRNP U2 [IDA]			266
Q5KP25 UniProt NPD GO	RSE1_CRYNE	Pre-mRNA-splicing factor RSE1	0.30	-	nuc	0	Nucleus (By similarity)				1217
Q5KND3 UniProt NPD GO	SLT11_CRYNE	Pre-mRNA-splicing factor SLT11	0.30	-	nuc	0	Nucleus (By similarity)				326
Q5D016 UniProt NPD GO	PFD1_BRARE	Prefoldin subunit 1	0.30	-	nuc	0					122
Q9NQP4 UniProt NPD GO	PFD4_HUMAN	Prefoldin subunit 4 (Protein C-1)	0.30	-	nuc	0		cytosol [NAS]	604898		134
P52553 UniProt NPD GO	PFD6_YEAST	Prefoldin subunit 6 (Genes involved in microtubule biogenesis protein 1) (Gim complex subunit 1) (Gi ...	0.30	-	nuc	0	Nucleus	cytoplasm [IDA] prefoldin complex [IPI]			114
P20742 UniProt NPD GO	PZP_HUMAN	Pregnancy zone protein precursor	0.30	-	nuc	0	Secreted protein	extracellular region [NAS]	176420		1482
Q00887 UniProt NPD GO	PSG9_HUMAN	Pregnancy-specific beta-1-glycoprotein 9 precursor (PSBG-9) (Pregnancy-specific glycoprotein 9) (Pre ...	0.30	-	nuc	0	Secreted protein (Potential)		176398		426
P40555 UniProt NPD GO	PSD9_YEAST	Probable 26S proteasome regulatory subunit p27 (Proteasome non-ATPase subunit 2)	0.30	-	nuc	0		cytoplasm [IDA]			220
Q6DWJ6 UniProt NPD GO	GP139_HUMAN	Probable G-protein coupled receptor 139 (G(q)-coupled orphan receptor GPRg1) (G-protein-coupled rece ...	0.30	-	end	7 *	Membrane; multi-pass membrane protein				353

You are viewing entries 40601 to 40650 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.