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
P53915 UniProt NPD GO	NRK1_YEAST	Nicotinamide riboside kinase 1 (EC 2.7.1.-)	0.27	-	mit	0		cytoplasm [IDA]			240
Q9C002 UniProt NPD GO	NMES1_HUMAN	Normal mucosa of esophagus-specific gene 1 protein (Protein FOAP-11)	0.27	-	cyt	1 *	Nucleus	nucleus [IDA]	608409		83
P46673 UniProt NPD GO	NUP85_YEAST	Nucleoporin NUP85 (Nuclear pore protein NUP85)	0.27	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			744
O88426 UniProt NPD GO	NDK6_RAT	Nucleoside diphosphate kinase 6 (EC 2.7.4.6) (NDK 6) (NDP kinase 6) (nm23-R6) (Fragment)	0.27	-	cyt	0					175
O13345 UniProt NPD GO	ORDA_ASPPA	O-methylsterigmatocystin oxidoreductase (EC 1.14.-.-) (OMST oxidoreductase) (Cytochrome P450 64)	0.27	-	nuc	1 *					528
P27116 UniProt NPD GO	DCOR_LEIDO	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.27	-	cyt	0					707
Q8J269 UniProt NPD GO	PYRF_PENNA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.27	-	mit	0					276
Q6DJ00 UniProt NPD GO	OSTC_XENTR	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.27	-	exc	0	Secreted protein (By similarity)				101
Q62170 UniProt NPD GO	SELPL_MOUSE	P-selectin glycoprotein ligand 1 precursor (PSGL-1) (Selectin P ligand)	0.27	-	exc	1	Membrane; single-pass type I membrane protein				397
P56277 UniProt NPD GO	MTCPA_HUMAN	P8 MTCP-1 protein (Mature T-cell proliferation-1 type A) (MTCP-1 type A) (P8MTCP1)	0.27	-	nuc	0	Mitochondrion		300116	2HP8	68
Q32PF3 UniProt NPD GO	PCNP_BOVIN	PEST proteolytic signal-containing nuclear protein (PEST-containing nuclear protein) (PCNP)	0.27	-	nuc	0	Nucleus (By similarity)				178
P32378 UniProt NPD GO	COQ2_YEAST	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.27	-	mit	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]			372
P01270 UniProt NPD GO	PTHY_HUMAN	Parathyroid hormone precursor (Parathyrin) (PTH) (Parathormone)	0.27	-	nuc	0	Secreted protein	extracellular region [NAS]	146200	1ZWG	115
Q56WK6 UniProt NPD GO	PATL1_ARATH	Patellin-1	0.27	-	cyt	0	Membrane. Cytoplasm. Mainly membrane-associated. Also cytoplasmic. Cell plate during cell division				573
O04681 UniProt NPD GO	PTI5_LYCES	Pathogenesis-related genes transcriptional activator PTI5 (PTO-interacting protein 5)	0.27	-	nuc	0	Nucleus				161
O24554 UniProt NPD GO	PEL_ZINEL	Pectate lyase precursor (EC 4.2.2.2) (ZePel)	0.27	-	mit	0					401
Q9GNK5 UniProt NPD GO	PGPLC_DROME	Peptidoglycan-recognition protein-LC (Immune response deficient 7 protein)	0.27	-	nuc	1	Membrane; single-pass type II membrane protein	integral to membrane [NAS]		2F2L	520
P91705 UniProt NPD GO	PER_DROSC	Period circadian protein (Fragment)	0.27	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				375
P21304 UniProt NPD GO	PWP1_YEAST	Periodic tryptophan protein 1	0.27	-	cyt	0		cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			576
Q2HJ56 UniProt NPD GO	PWP1_BOVIN	Periodic tryptophan protein 1 homolog	0.27	+	mit	0	Nucleus (By similarity)				500
Q8BU03 UniProt NPD GO	PWP2_MOUSE	Periodic tryptophan protein 2 homolog	0.27	-	nuc	0	Nucleus; nucleolus (By similarity)				919
Q9LHB9 UniProt NPD GO	PER32_ARATH	Peroxidase 32 precursor (EC 1.11.1.7) (Atperox P32) (PRXR3) (ATP16a)	0.27	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				352
P15233 UniProt NPD GO	PER1C_ARMRU	Peroxidase C1C precursor (EC 1.11.1.7) (Fragment)	0.27	-	mit	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				332
Q9Z210 UniProt NPD GO	PX11B_MOUSE	Peroxisomal membrane protein 11B (Peroxin-11B) (Peroxisomal biogenesis factor 11B) (PEX11beta) (Pex1 ...	0.27	-	nuc	1	Peroxisome (By similarity)	mitochondrion [IDA]			259
Q5RFI0 UniProt NPD GO	PX11B_PONPY	Peroxisomal membrane protein 11B (Peroxin-11B) (Peroxisomal biogenesis factor 11B) (PEX11beta) (Pex1 ...	0.27	-	nuc	1	Peroxisome (By similarity)				259
Q99LC9 UniProt NPD GO	PEX6_MOUSE	Peroxisome assembly factor 2 (PAF-2) (Peroxisomal-type ATPase 1) (Peroxin-6) (Peroxisomal biogenesis ...	0.27	-	cyt	0	Cytoplasm. Peroxisome; peroxisomal membrane. Associated with peroxisomal membranes				981
P81131 UniProt NPD GO	PER1_VOLCA	Perphorin-1 precursor (Perphorin I)	0.27	-	exc	0	Secreted protein; extracellular space; extracellular matrix				512
P45734 UniProt NPD GO	PALY_TRISU	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.27	-	nuc	0	Cytoplasm (Probable)				725
Q9M568 UniProt NPD GO	PAL1_RUBID	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5) (RiPAL1)	0.27	-	nuc	0	Cytoplasm (Probable)				710
P19142 UniProt NPD GO	PAL2_PHAVU	Phenylalanine ammonia-lyase class 2 (EC 4.3.1.5) (Phenylalanine ammonia-lyase class II)	0.27	-	nuc	0	Cytoplasm (Probable)				712
O42870 UniProt NPD GO	SYFA_SCHPO	Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase alpha chain) (Phe ...	0.27	-	cyt	0	Cytoplasm (By similarity)				499
Q5RB77 UniProt NPD GO	PDCL3_PONPY	Phosducin-like protein 3	0.27	-	cyt	0	Cytoplasm (By similarity)				239
Q80XI4 UniProt NPD GO	PI52B_MOUSE	Phosphatidylinositol-4-phosphate 5-kinase type-2 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.27	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...				416
O88377 UniProt NPD GO	PI52B_RAT	Phosphatidylinositol-4-phosphate 5-kinase type-2 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.27	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...				416
P20474 UniProt NPD GO	PA21B_BOTAS	Phospholipase A2 (EC 3.1.1.4) (Myotoxin I) (Phosphatidylcholine 2-acylhydrolase)	0.27	-	nuc	0	Secreted protein				122
Q15126 UniProt NPD GO	PMVK_HUMAN	Phosphomevalonate kinase (EC 2.7.4.2) (PMKase)	0.27	-	cyt	0	Peroxisome	peroxisome [TAS]	607622		191
Q16816 UniProt NPD GO	PHKG1_HUMAN	Phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (EC 2.7.11.19) (Phosphorylase ...	0.27	-	cyt	0			172470		386
Q70Y02 UniProt NPD GO	YCF3_AMBTC	Photosystem I assembly protein ycf3	0.27	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q6YXP2 UniProt NPD GO	YCF3_PHYPA	Photosystem I assembly protein ycf3	0.27	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q8WI17 UniProt NPD GO	YCF3_PSINU	Photosystem I assembly protein ycf3	0.27	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				171
P93673 UniProt NPD GO	PHYA_LATSA	Phytochrome type A	0.27	-	mit	0					1124
O70176 UniProt NPD GO	PACA_MOUSE	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP) [Contains: PACAP-related peptid ...	0.27	-	nuc	0	Secreted protein				175
P05030 UniProt NPD GO	PMA1_YEAST	Plasma membrane ATPase 1 (EC 3.6.3.6) (Proton pump 1)	0.27	+	end	10	Cell membrane; multi-pass membrane protein	lipid raft [IDA] plasma membrane [IDA]			918
P23980 UniProt NPD GO	PMA2_LYCES	Plasma membrane ATPase 2 (EC 3.6.3.6) (Proton pump 2) (Fragment)	0.27	-	end	6 *	Cell membrane; multi-pass membrane protein				704
P23634 UniProt NPD GO	AT2B4_HUMAN	Plasma membrane calcium-transporting ATPase 4 (EC 3.6.3.8) (PMCA4) (Plasma membrane calcium pump iso ...	0.27	-	end	8	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	108732	1CFF	1241
P46296 UniProt NPD GO	RR12_CUSEU	Plastid 30S ribosomal protein S12	0.27	-	mit	0	Plastid				123
P40197 UniProt NPD GO	GPV_HUMAN	Platelet glycoprotein V precursor (GPV) (CD42D antigen)	0.27	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	173511		560
Q9GK76 UniProt NPD GO	PTAFR_CAPHI	Platelet-activating factor receptor (PAF-R) (PAFr)	0.27	-	end	7 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			342
Q9DC11 UniProt NPD GO	PXDC2_MOUSE	Plexin domain-containing protein 2 precursor (Tumor endothelial marker 7-related protein)	0.27	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				530
P57721 UniProt NPD GO	PCBP3_HUMAN	Poly(rC)-binding protein 3 (Alpha-CP3)	0.27	-	nuc	0	Cytoplasm		608502		339

You are viewing entries 43451 to 43500 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.