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
Q09525 UniProt NPD GO	PME2_CAEEL	Poly(ADP-ribose) polymerase pme-2 (EC 2.4.2.30) (Poly ADP-ribose metabolism enzyme 2)	0.29	+	cyt	0	Nucleus (Probable)				538
Q28ZX3 UniProt NPD GO	PABP2_DROPS	Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (Poly(A)-binding protein II) (PABII) (Po ...	0.29	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm b ...	cytoplasm [ISS] nucleus [ISS]			225
Q6WV19 UniProt NPD GO	GALT2_DROME	Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.29	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			633
Q08296 UniProt NPD GO	PPOF_LYCES	Polyphenol oxidase F, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.29	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				585
Q9ZP19 UniProt NPD GO	PPO1_IPOBA	Polyphenol oxidase I, chloroplast (EC 1.10.3.1) (PPO-I) (Catechol oxidase I)	0.29	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)			1BUG	496
Q8WN55 UniProt NPD GO	PTBP1_BOVIN	Polypyrimidine tract-binding protein 1 (PTB)	0.29	-	nuc	0	Nucleus (By similarity)				531
Q67VS5 UniProt NPD GO	HAK10_ORYSA	Potassium transporter 10 (OsHAK10)	0.29	+	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein. May localize to tonoplast				843
P17972 UniProt NPD GO	KCNAW_DROME	Potassium voltage-gated channel protein Shaw (Shaw2)	0.29	+	vac	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]			498
P10499 UniProt NPD GO	KCNA1_RAT	Potassium voltage-gated channel subfamily A member 1 (Voltage-gated potassium channel subunit Kv1.1) ...	0.29	-	end	4	Membrane; multi-pass membrane protein			1EXB	495
P22739 UniProt NPD GO	KCNA2_XENLA	Potassium voltage-gated channel subfamily A member 2 (Voltage-gated potassium channel subunit Kv1.2) ...	0.29	-	end	5	Membrane; multi-pass membrane protein				499
P50638 UniProt NPD GO	KCNA5_RABIT	Potassium voltage-gated channel subfamily A member 5 (Voltage-gated potassium channel subunit Kv1.5) ...	0.29	-	end	3	Membrane; multi-pass membrane protein				598
O74970 UniProt NPD GO	PRP39_SCHPO	Pre-mRNA-processing protein prp39	0.29	-	cyt	0	Nucleus (By similarity)				612
Q6FLQ6 UniProt NPD GO	RSE1_CANGA	Pre-mRNA-splicing factor RSE1	0.29	-	mit	0	Nucleus (By similarity)				1296
Q52E49 UniProt NPD GO	RSE1_MAGGR	Pre-mRNA-splicing factor RSE1	0.29	-	cyt	0	Nucleus (By similarity)				1229
P43589 UniProt NPD GO	SAD1_YEAST	Pre-mRNA-splicing factor SAD1 (snRNP assembly-defective protein 1)	0.29	-	nuc	0	Nucleus	nucleus [IDA]			448
Q7RYR4 UniProt NPD GO	RSE1_NEUCR	Pre-mRNA-splicing factor rse-1	0.29	-	cyt	0	Nucleus (By similarity)				1271
Q5B1X8 UniProt NPD GO	RSE1_EMENI	Pre-mRNA-splicing factor rse1	0.29	-	cyt	0	Nucleus (By similarity)				1226
Q15235 UniProt NPD GO	PSG10_HUMAN	Pregnancy-specific beta-1-glycoprotein 10 precursor (PSBG-10) (PSBG-12)	0.29	-	nuc	0	Secreted protein (Potential)	extracellular region [NAS]	176399		424
Q16557 UniProt NPD GO	PSG3_HUMAN	Pregnancy-specific beta-1-glycoprotein 3 precursor (PSBG-3) (Carcinoembryonic antigen SG5)	0.29	-	nuc	0	Secreted protein (Potential)	extracellular region [NAS]	176392		428
Q00889 UniProt NPD GO	PSG6_HUMAN	Pregnancy-specific beta-1-glycoprotein 6 precursor (PSBG-6)	0.29	-	nuc	0	Secreted protein (Potential)		176395		435
Q5RDB1 UniProt NPD GO	MOB3_PONPY	Preimplantation protein 3 (Mps one binder kinase activator-like 3) (Mob1 homolog 3) (Mob3)	0.29	-	nuc	0	Cytoplasm; perinuclear region. Membrane; peripheral membrane protein. Golgi apparatus; Golgi stack; ...				225
Q6PEB6 UniProt NPD GO	MOB3_MOUSE	Preimplantation protein 3 (Mps one binder kinase activator-like 3) (Mob1 homolog 3) (Mob3) (Class II ...	0.29	-	nuc	0	Cytoplasm; perinuclear region. Membrane; peripheral membrane protein. Golgi apparatus; Golgi stack; ...				225
Q9Y3A3 UniProt NPD GO	MOB3_HUMAN	Preimplantation protein 3 (Mps one binder kinase activator-like 3) (Mob1 homolog 3) (Mob3) (Class II ...	0.29	-	nuc	0	Cytoplasm; perinuclear region. Membrane; peripheral membrane protein. Golgi apparatus; Golgi stack; ...		609361		225
Q9QYW3 UniProt NPD GO	MOB3_RAT	Preimplantation protein 3 (Mps one binder kinase activator-like 3) (Mob1 homolog 3) (Mob3) (Class II ...	0.29	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus; Golgi stack; Golgi stack membrane ...	membrane fraction [IDA]			225
P54823 UniProt NPD GO	DDX6_MOUSE	Probable ATP-dependent RNA helicase DDX6 (EC 3.6.1.-) (DEAD box protein 6) (ATP-dependent RNA helica ...	0.29	-	nuc	0	Cytoplasm (By similarity). Processing bodies (PB) (By similarity)				483
O74841 UniProt NPD GO	FAD1_SCHPO	Probable FAD synthetase (EC 2.7.7.2) (FMN adenylyltransferase) (FAD pyrophosphorylase) (Flavin adeni ...	0.29	-	nuc	0					265
Q80UC8 UniProt NPD GO	GP139_MOUSE	Probable G-protein coupled receptor 139 (G(q)-coupled orphan receptor GPRg1) (G-protein-coupled rece ...	0.29	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			345
Q64017 UniProt NPD GO	GP176_RAT	Probable G-protein coupled receptor 176 (G-protein coupled receptor AGR9) (RBU-15)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				513
Q9LF64 UniProt NPD GO	ATL5G_ARATH	Probable RING-H2 finger protein ATL5G	0.29	-	nuc	1					362
P78750 UniProt NPD GO	UTP18_SCHPO	Probable U3 small nucleolar RNA-associated protein 18 (U3 snoRNA-associated protein 18)	0.29	-	cyt	0	Nucleus; nucleolus (By similarity)				556
P52290 UniProt NPD GO	PPAD_YEAST	Probable acid phosphatase DIA3 precursor (EC 3.1.3.2)	0.29	-	cyt	0		cell wall (sensu Fungi) [IDA]			468
P34355 UniProt NPD GO	ACOX_CAEEL	Probable acyl-coenzyme A oxidase, peroxisomal (EC 1.3.3.6) (Acyl-CoA oxidase) (AOX)	0.29	-	pox	0	Peroxisome (By similarity)				659
Q09679 UniProt NPD GO	GMH1_SCHPO	Probable alpha-1,2-galactosyltransferase gmh1 (EC 2.4.1.-)	0.29	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				329
P40439 UniProt NPD GO	MALX2_YEAST	Probable alpha-glucosidase YIL172C/YJL221C (EC 3.2.1.20) (Maltase)	0.29	-	cyt	0		cytoplasm [IDA]			589
Q20799 UniProt NPD GO	CMC2_CAEEL	Probable calcium-binding mitochondrial carrier F55A11.4	0.29	+	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				588
Q65X71 UniProt NPD GO	ACA6_ORYSA	Probable calcium-transporting ATPase 6, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 6)	0.29	+	end	10	Membrane; multi-pass membrane protein (By similarity)				1021
Q7XWP1 UniProt NPD GO	CPSF1_ORYSA	Probable cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit)	0.29	-	cyt	0	Nucleus (By similarity)				1441
Q86ZL5 UniProt NPD GO	ATG4_PODAN	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.29	-	nuc	0	Cytoplasm (By similarity)				500
Q7S3X7 UniProt NPD GO	ATG4_NEUCR	Probable cysteine protease atg-4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.29	-	nuc	0	Cytoplasm (By similarity)				506
Q9V6D6 UniProt NPD GO	CP301_DROME	Probable cytochrome P450 301a1, mitochondrial precursor (EC 1.14.-.-) (CYPCCCIA1)	0.29	-	nuc	0	Mitochondrion (Potential)				553
Q18164 UniProt NPD GO	DPYD_CAEEL	Probable dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2) (DPD) (DHPDHase) (Dihydrouracil dehydr ...	0.29	-	nuc	0					1059
P53189 UniProt NPD GO	SCW11_YEAST	Probable family 17 glucosidase SCW11 precursor (EC 3.2.1.-) (Soluble cell wall protein 11)	0.29	-	nuc	0	Cell wall	cell wall (sensu Fungi) [IDA]			542
Q9SJP4 UniProt NPD GO	FUT5_ARATH	Probable fucosyltransferase 5 (EC 2.4.1.-) (AtFUT5)	0.29	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				533
P0C0M3 UniProt NPD GO	GH311_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.11 (EC 6.3.2.-) (Auxin-responsive GH3-like protei ...	0.29	-	cyt	0					591
Q60EY1 UniProt NPD GO	GH36_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.6 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.29	-	cyt	0					488
Q6FN12 UniProt NPD GO	SPC24_CANGA	Probable kinetochore protein SPC24	0.29	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				201
Q8VDC0 UniProt NPD GO	SYLM_MOUSE	Probable leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS) ...	0.29	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				902
Q9VHD3 UniProt NPD GO	MAAI1_DROME	Probable maleylacetoacetate isomerase 1 (EC 5.2.1.2) (MAAI 1)	0.29	-	mit	0	Cytoplasm (By similarity)				246
Q8T3L6 UniProt NPD GO	FABD_DROME	Probable malonyl CoA-acyl carrier protein transacylase, mitochondrial precursor (EC 2.3.1.39) (MCT)	0.29	-	mit	0	Mitochondrion (Probable)	mitochondrion [ISS]			379
Q5AI37 UniProt NPD GO	ARX1_CANAL	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.29	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				564

You are viewing entries 41601 to 41650 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.