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
P46970 UniProt NPD GO	NMD5_YEAST	Nonsense-mediated mRNA decay protein 5	0.43	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			1048
Q09684 UniProt NPD GO	THT1_SCHPO	Nuclear fusion protein tht1	0.43	-	end	3	Membrane; multi-pass membrane protein (Potential)	nuclear membrane [IDA]			577
Q9GYU8 UniProt NPD GO	NUP88_DROME	Nuclear pore complex protein Nup88 (Nucleoporin Nup88) (88 kDa nuclear pore complex protein) (dNup88 ...	0.43	-	end	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side	nuclear envelope [IDA] nuclear pore [IDA]			702
Q61066 UniProt NPD GO	DAX1_MOUSE	Nuclear receptor 0B1 (Nuclear receptor DAX-1)	0.43	-	pox	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			472
P63139 UniProt NPD GO	NFYB_MOUSE	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.43	-	nuc	0	Nucleus	transcription factor complex [IC]			207
P63140 UniProt NPD GO	NFYB_RAT	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.43	-	nuc	0	Nucleus				207
Q6AXN4 UniProt NPD GO	NDC1_RAT	Nucleoporin NDC1 (Transmembrane protein 48)	0.43	-	end	5 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				673
Q9JL35 UniProt NPD GO	NSBP1_MOUSE	Nucleosome-binding protein 1 (Nucleosome-binding protein 45) (NBP-45) (GARP45 protein)	0.43	-	nuc	0	Nucleus	nucleoplasm [IDA]			406
Q06666 UniProt NPD GO	T2_MOUSE	Octapeptide-repeat protein T2	0.43	+	nuc	0					185
Q9D8S4 UniProt NPD GO	ORN_MOUSE	Oligoribonuclease, mitochondrial precursor (EC 3.1.-.-) (Small fragment nuclease) (RNA exonuclease 2 ...	0.43	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			237
Q5U1X1 UniProt NPD GO	ORN_RAT	Oligoribonuclease, mitochondrial precursor (EC 3.1.-.-) (Small fragment nuclease) (RNA exonuclease 2 ...	0.43	-	mit	0	Mitochondrion (By similarity)				237
P18752 UniProt NPD GO	ZO72_XENLA	Oocyte zinc finger protein XLCOF7.2 (Fragment)	0.43	-	nuc	0	Nucleus (Potential)				391
Q9Y1B2 UniProt NPD GO	ORC6_DROME	Origin recognition complex subunit 6	0.43	-	nuc	0	Nucleus (By similarity)	nuclear origin of replication recognition c... [IDA]			257
P54368 UniProt NPD GO	OAZ1_HUMAN	Ornithine decarboxylase antizyme (ODC-Az)	0.43	-	mit	0			601579		227
Q8MIM3 UniProt NPD GO	NR1I3_MACMU	Orphan nuclear receptor NR1I3 (Constitutive androstane receptor) (CAR)	0.43	-	cyt	0	Nucleus (By similarity)				352
Q9YGL3 UniProt NPD GO	NR2E1_ORYLA	Orphan nuclear receptor NR2E1 (Nuclear receptor TLX) (Tailless homolog) (Tll)	0.43	-	nuc	0	Nucleus (By similarity)				396
Q62010 UniProt NPD GO	OVGP1_MOUSE	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.43	-	cyt	0	Secretory granules				721
P09971 UniProt NPD GO	PBAN_BOMMO	PBAN-type neuropeptides precursor [Contains: Diapause hormone (DH); Alpha-SG neuropeptide (Alpha-SGN ...	0.43	-	exc	1 *	Secreted protein				192
Q9GKU1 UniProt NPD GO	PDLI2_MACFA	PDZ and LIM domain protein 2	0.43	-	nuc	0	Cytoplasm. Cytoskeleton. Localizes at the cytoskeleton. Colocalizes with beta-1 integrin (ITGB1) and ...				352
P38126 UniProt NPD GO	PCH2_YEAST	Pachytene checkpoint protein 2	0.43	-	nuc	0	Nucleus	nucleolus [TAS]			536
Q8VI59 UniProt NPD GO	PCX3_MOUSE	Pecanex-like protein 3	0.43	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1620
Q96L50 UniProt NPD GO	LLR1_HUMAN	Peptidylprolyl isomerase-like 5 (LRR-repeat protein 1) (LRR-1) (4-1BB-mediated signaling molecule) ( ...	0.43	-	nuc	0			609193		414
Q9M9Q9 UniProt NPD GO	PER5_ARATH	Peroxidase 5 precursor (EC 1.11.1.7) (Atperox P5)	0.43	-	mit	0	Secreted protein (By similarity)				321
Q9LVL2 UniProt NPD GO	PER67_ARATH	Peroxidase 67 precursor (EC 1.11.1.7) (Atperox P67) (ATP44)	0.43	-	exc	0	Secreted protein (By similarity)				316
Q6CT48 UniProt NPD GO	PEX5_KLULA	Peroxisomal targeting signal receptor (Peroxin-5) (PTS1 receptor)	0.43	+	nuc	0	Cytoplasm (By similarity). Peroxisome; peroxisomal membrane; peripheral membrane protein (By similar ...				566
P33292 UniProt NPD GO	PEX5_PICPA	Peroxisomal targeting signal receptor (Peroxisomal protein PAS8) (Peroxin-5) (PTS1 receptor)	0.43	-	nuc	0	Cytoplasm. Peroxisome; peroxisomal membrane; peripheral membrane protein. Its distribution appears t ...				576
P06842 UniProt NPD GO	STE2_YEAST	Pheromone alpha factor receptor	0.43	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			431
P50520 UniProt NPD GO	VPS34_SCHPO	Phosphatidylinositol 3-kinase vps34 (EC 2.7.1.137) (PtdIns-3-kinase vps34) (PI3-kinase vps34) (PI3K ...	0.43	-	mit	0					801
Q9Z1L0 UniProt NPD GO	PK3CB_RAT	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta isoform (EC 2.7.1.153) (PI3-ki ...	0.43	-	nuc	0					1070
O48709 UniProt NPD GO	PI5K3_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 3 (EC 2.7.1.68) (AtPIP5K3) (1-phosphatidylinositol-4-phosp ...	0.43	-	cyt	0					705
P29976 UniProt NPD GO	AROF_ARATH	Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.43	-	cyt	0	Plastid; chloroplast				525
Q7TSH2 UniProt NPD GO	KPBB_MOUSE	Phosphorylase b kinase regulatory subunit beta (Phosphorylase kinase subunit beta)	0.43	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1085
P62721 UniProt NPD GO	YCF4_PINKO	Photosystem I assembly protein ycf4	0.43	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P41620 UniProt NPD GO	YCF4_PINTH	Photosystem I assembly protein ycf4	0.43	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P51365 UniProt NPD GO	PYG_PORPU	Phycobilisome rod-core linker polypeptide cpcG	0.43	-	cyt	0	Plastid; chloroplast				230
P06592 UniProt NPD GO	PHYA_CUCPE	Phytochrome A	0.43	-	mit	0					1124
P06867 UniProt NPD GO	PLMN_PIG	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Plasmin he ...	0.43	-	nuc	0	Secreted protein				790
P32760 UniProt NPD GO	PTN_CHICK	Pleiotrophin (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding growth fac ...	0.43	-	nuc	0	Secreted protein				136
O43157 UniProt NPD GO	PLXB1_HUMAN	Plexin-B1 precursor (Semaphorin receptor SEP)	0.43	-	end	0	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3: Secreted protei ...	integral to plasma membrane [NAS]	601053		2135
O00592 UniProt NPD GO	PODXL_HUMAN	Podocalyxin-like protein 1 precursor	0.43	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	602632		528
P26446 UniProt NPD GO	PARP1_CHICK	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase 1) (Pol ...	0.43	+	nuc	0	Nucleus			4PAX	1011
Q9NRJ5 UniProt NPD GO	PAPOB_HUMAN	Poly(A) polymerase beta (EC 2.7.7.19) (PAP beta) (Polynucleotide adenylyltransferase beta) (Testis-s ...	0.43	-	cyt	0	Nucleus (Probable)		607436		636
Q13310 UniProt NPD GO	PABP4_HUMAN	Polyadenylate-binding protein 4 (Poly(A)-binding protein 4) (PABP 4) (Inducible poly(A)-binding prot ...	0.43	-	nuc	0	Cytoplasm	cytoplasm [IDA]	603407		644
O88422 UniProt NPD GO	GALT5_RAT	Polypeptide N-acetylgalactosaminyltransferase 5 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.43	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				930
O16846 UniProt NPD GO	TXHMK_RADMG	Potassium channel toxin HmK precursor	0.43	-	exc	1 *	Secreted protein (Probable). Found in nematocyst (Probable)				74
Q9WVJ0 UniProt NPD GO	KCNH3_MOUSE	Potassium voltage-gated channel subfamily H member 3 (Voltage-gated potassium channel subunit Kv12.2 ...	0.43	-	end	4	Membrane; multi-pass membrane protein				1087
Q8NCM2 UniProt NPD GO	KCNH5_HUMAN	Potassium voltage-gated channel subfamily H member 5 (Voltage-gated potassium channel subunit Kv10.2 ...	0.43	-	end	4	Membrane; multi-pass membrane protein		605716		988
Q9EPI9 UniProt NPD GO	KCNH5_RAT	Potassium voltage-gated channel subfamily H member 5 (Voltage-gated potassium channel subunit Kv10.2 ...	0.43	-	end	4	Membrane; multi-pass membrane protein				988
P51787 UniProt NPD GO	KCNQ1_HUMAN	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.43	-	end	6	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	609621		676
Q6CPC3 UniProt NPD GO	FIP1_KLULA	Pre-mRNA polyadenylation factor FIP1	0.43	-	nuc	0	Nucleus (By similarity)				295

You are viewing entries 29851 to 29900 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.