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
P83870 UniProt NPD GO	PHF5A_MOUSE	PHD finger-like domain protein 5A (Splicing factor 3B-associated 14 kDa protein) (SF3b14b)	0.15	-	nuc	0	Nucleus	nuclear matrix [IDA] snRNP U2 [ISS]			110
Q7RTV0 UniProt NPD GO	PHF5A_HUMAN	PHD finger-like domain-containing protein 5A (PHD finger-like domain protein 5A) (Splicing factor 3B ...	0.15	-	nuc	0	Nucleus (By similarity)	snRNP U2 [IDA]			110
P83871 UniProt NPD GO	PHF5A_RAT	PHD finger-like domain-containing protein 5A (PHD finger-like domain protein 5A) (Splicing factor 3B ...	0.15	-	nuc	0	Nucleus	snRNP U2 [ISS]			110
Q9D733 UniProt NPD GO	GP2_MOUSE	Pancreatic secretory granule membrane major glycoprotein GP2 precursor (Pancreatic zymogen granule m ...	0.15	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Secreted protein (By similarity). Secreted ...				531
P14280 UniProt NPD GO	PME1_LYCES	Pectinesterase-1 precursor (EC 3.1.1.11) (Pectin methylesterase 1) (PE 1)	0.15	-	mit	1 *	Cell wall			1XG2	546
P09607 UniProt NPD GO	PME21_LYCES	Pectinesterase-2 precursor (EC 3.1.1.11) (Pectin methylesterase 2) (PE 2)	0.15	-	mit	1 *	Cell wall				550
Q5MFV8 UniProt NPD GO	PME5_ARATH	Pectinesterase-5 precursor (EC 3.1.1.11) (Pectin methylesterase 5) (PE 5) (VANGUARD 1 protein)	0.15	-	cyt	1 *	Distributed in the whole pollen tube, including the plasma membrane and pollen tube wall				595
O43511 UniProt NPD GO	S26A4_HUMAN	Pendrin (Sodium-independent chloride/iodide transporter) (Solute carrier family 26 member 4)	0.15	-	end	9	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]	605646		780
P00790 UniProt NPD GO	PEPA_HUMAN	Pepsin A precursor (EC 3.4.23.1)	0.15	-	exc	0	Secreted protein		169700	1QRP	388
P00791 UniProt NPD GO	PEPA_PIG	Pepsin A precursor (EC 3.4.23.1)	0.15	-	exc	0	Secreted protein			5PEP	386
P03954 UniProt NPD GO	PEPA1_MACFU	Pepsin A-1 precursor (EC 3.4.23.1) (Pepsin III-3)	0.15	-	exc	0	Secreted protein				388
P28712 UniProt NPD GO	PEPA1_RABIT	Pepsin II-1 precursor (EC 3.4.23.1) (Pepsin A)	0.15	-	exc	0	Secreted protein				387
Q9TR93 UniProt NPD GO	PYY_RABIT	Peptide YY (PYY) (PYY-I) (Peptide tyrosine tyrosine) [Contains: Peptide YY(3-36) (PYY-II)]	0.15	-	nuc	0	Secreted protein				36
P84006 UniProt NPD GO	PYF2_PENMO	Peptide tyrosine phenylalanine 2 (Pem-PYF2)	0.15	-		0	Secreted protein				9
P84008 UniProt NPD GO	PYF4_PENMO	Peptide tyrosine phenylalanine 4 (Pem-PYF4)	0.15	-		0	Secreted protein				9
Q26516 UniProt NPD GO	PPIE_SCHJA	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) (PPIase E) (Rotamase E) (Cyclophilin E) (Fragment ...	0.15	-	cyt	0	Cytoplasm				179
O49939 UniProt NPD GO	TLP40_SPIOL	Peptidyl-prolyl cis-trans isomerase, chloroplast precursor (EC 5.2.1.8) (40 kDa thylakoid lumen PPIa ...	0.15	+	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen. Can interact with the inner surface of the stroma ...				449
P34222 UniProt NPD GO	PTH2_YEAST	Peptidyl-tRNA hydrolase 2 (EC 3.1.1.29) (PTH 2)	0.15	-	mit	1 *	Cytoplasm	cytoplasm [IC] mitochondrial outer membrane [IDA] mitochondrion [IDA]			214
Q96506 UniProt NPD GO	PER1_ARATH	Peroxidase 1/2 precursor (EC 1.11.1.7) (Atperox P1/P2) (ATP11a)	0.15	-	exc	1 *	Secreted protein (By similarity)				325
Q9FMR0 UniProt NPD GO	PER60_ARATH	Peroxidase 60 precursor (EC 1.11.1.7) (Atperox P60) (ATP14a)	0.15	-	exc	0	Secreted protein (By similarity)				331
Q9DBM2 UniProt NPD GO	ECHP_MOUSE	Peroxisomal bifunctional enzyme (PBE) (PBFE) [Includes: Enoyl-CoA hydratase (EC 4.2.1.17); 3,2-trans ...	0.15	-	pox	0	Peroxisome (By similarity)	mitochondrion [IDA] peroxisome [TAS]			717
O19094 UniProt NPD GO	OCTC_BOVIN	Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) (COT)	0.15	-	cyt	0	Peroxisome (Potential)				612
Q29RU9 UniProt NPD GO	SOX_BOVIN	Peroxisomal sarcosine oxidase (EC 1.5.3.1) (PSO) (L-pipecolate oxidase) (EC 1.5.3.7) (L-pipecolic ac ...	0.15	-	mit	0	Peroxisome (By similarity)				392
Q9D826 UniProt NPD GO	SOX_MOUSE	Peroxisomal sarcosine oxidase (EC 1.5.3.1) (PSO) (L-pipecolate oxidase) (EC 1.5.3.7) (L-pipecolic ac ...	0.15	-	mit	0	Peroxisome (By similarity)				390
Q13608 UniProt NPD GO	PEX6_HUMAN	Peroxisome assembly factor 2 (PAF-2) (Peroxisomal-type ATPase 1) (Peroxin-6) (Peroxisomal biogenesis ...	0.15	-	cyt	0	Cytoplasm. Peroxisome; peroxisomal membrane. Associated with peroxisomal membranes	cytoplasm [TAS]	601498		980
P53443 UniProt NPD GO	PAL2_ORYSA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.15	-	nuc	0	Cytoplasm (Probable)				713
Q9SS45 UniProt NPD GO	PAL4_ARATH	Phenylalanine ammonia-lyase 4 (EC 4.3.1.5)	0.15	-	cyt	0	Cytoplasm (Probable)				707
O13432 UniProt NPD GO	SYFB_CANAL	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.15	-	cyt	0	Cytoplasm				592
P31397 UniProt NPD GO	MAP3_SCHPO	Pheromone M-factor receptor	0.15	-	end	6 *	Membrane; multi-pass membrane protein				365
O80400 UniProt NPD GO	VPS_HUMLU	Phloroisovalerophenone synthase (EC 2.3.1.156) (Valerophenone synthase) (3-methyl-1-(trihydroxypheny ...	0.15	-	nuc	0					394
Q32LN3 UniProt NPD GO	PDCL2_BOVIN	Phosducin-like protein 2	0.15	-	cyt	0					242
Q05924 UniProt NPD GO	DCR2_YEAST	Phosphatase DCR2 (EC 3.1.-.-) (Dosage-dependent cell cycle regulator 2)	0.15	-	mit	1 *	Cytoplasm				578
Q9BRB3 UniProt NPD GO	PIGQ_HUMAN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q (EC 2.4.1.198) (Phosphatidylinositol- ...	0.15	-	end	4	Membrane; multi-pass membrane protein (Potential)		605754		759
P53860 UniProt NPD GO	PDR16_YEAST	Phosphatidylinositol transfer protein PDR16 (PITP) (Pleiotropic drug resistance protein 16) (SEC14 h ...	0.15	-	cyt	0	Lipid particle; lipid particle membrane; peripheral membrane protein. Microsome; microsomal membrane ...	cytoplasm [IDA] lipid particle [IDA] microsome [IDA]			351
P00612 UniProt NPD GO	PA23_LATSE	Phospholipase A2 isozyme 3 (EC 3.1.1.4) (Phospholipase A2 isozyme III) (Phosphatidylcholine 2-acylhy ...	0.15	-	nuc	0	Secreted protein				118
Q9DF56 UniProt NPD GO	PA23_OPHHA	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.15	-	exc	0	Secreted protein (By similarity)				152
Q7M334 UniProt NPD GO	PA2_RABIT	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.15	-	exc	0	Secreted protein (By similarity)				144
Q9JJ00 UniProt NPD GO	PLS1_MOUSE	Phospholipid scramblase 1 (PL scramblase 1) (Ca(2+)-dependent phospholipid scramblase 1) (Transplant ...	0.15	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				328
Q3SZJ9 UniProt NPD GO	PMM2_BOVIN	Phosphomannomutase 2 (EC 5.4.2.8) (PMM 2)	0.15	-	cyt	0	Cytoplasm (By similarity)				246
P38025 UniProt NPD GO	PUR7_ARATH	Phosphoribosylaminoimidazole-succinocarboxamide synthase, chloroplast precursor (EC 6.3.2.6) (SAICAR ...	0.15	-	mit	0	Plastid; chloroplast (Probable)				411
Q9VSY6 UniProt NPD GO	SERB_DROME	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase)	0.15	-	mit	0					270
Q96BW5 UniProt NPD GO	PTER_HUMAN	Phosphotriesterase-related protein (Parathion hydrolase-related protein) (HPHRP)	0.15	-	cyt	0			604446		349
P36213 UniProt NPD GO	PSAD_HORVU	Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI- ...	0.15	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side				205
O65107 UniProt NPD GO	PSAN_MAIZE	Photosystem I reaction center subunit N, chloroplast precursor (PSI-N) (Fragment)	0.15	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side				112
O18778 UniProt NPD GO	PAHX_BOVIN	Phytanoyl-CoA dioxygenase, peroxisomal precursor (EC 1.14.11.18) (Phytanoyl-CoA alpha-hydroxylase) ( ...	0.15	-	mit	0	Peroxisome				337
P49086 UniProt NPD GO	CRTI_MAIZE	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.15	-	nuc	0	Plastid; chloroplast. Plastid; chromoplast				571
P58136 UniProt NPD GO	RR11_ASTLO	Plastid 30S ribosomal protein S11	0.15	+	cyt	0	Plastid				112
Q85UK6 UniProt NPD GO	RK22_OROMI	Plastid 50S ribosomal protein L22	0.15	-	nuc	0	Plastid				150
P30068 UniProt NPD GO	RK33_EPIVI	Plastid 50S ribosomal protein L33	0.15	-	nuc	0	Plastid				66
P24355 UniProt NPD GO	RK36_ASTLO	Plastid 50S ribosomal protein L36	0.15	-	mit	0	Plastid				37

You are viewing entries 57351 to 57400 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.