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
P50689 UniProt NPD GO	COX2_GEOCP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37548 UniProt NPD GO	COX2_MACCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P04373 UniProt NPD GO	COX2_ORYSA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
P00406 UniProt NPD GO	COX2_RAT	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q02226 UniProt NPD GO	COXT_SOYBN	Cytochrome c oxidase subunit 2, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase polypepti ...	0.07	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				394
O46584 UniProt NPD GO	COX41_AOTAZ	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.07	-	nuc	1	Mitochondrion; mitochondrial inner membrane				144
O46578 UniProt NPD GO	COX41_GORGO	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.07	-	nuc	1	Mitochondrion; mitochondrial inner membrane				144
O46580 UniProt NPD GO	COX41_HYLAG	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.07	-	nuc	1	Mitochondrion; mitochondrial inner membrane				144
O46582 UniProt NPD GO	COX41_SAISC	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.07	-	nuc	1	Mitochondrion; mitochondrial inner membrane				124
P00423 UniProt NPD GO	COX41_BOVIN	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.07	-	mit	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IDA]		2OCC	169
P19783 UniProt NPD GO	COX41_MOUSE	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.07	-	nuc	1	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			169
Q6FWE8 UniProt NPD GO	COX9_CANGA	Cytochrome c oxidase subunit 7A precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIA)	0.07	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				59
O94705 UniProt NPD GO	COX9_SCHPO	Cytochrome c oxidase subunit 7A precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIA)	0.07	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				57
O98448 UniProt NPD GO	CY550_THAWE	Cytochrome c-550 (Cytochrome c550) (Fragment)	0.07	-	nuc	0	Plastid; chloroplast				80
Q9FIA0 UniProt NPD GO	CNGT2_ARATH	Cytokinin-N-glucosyltransferase 2 (EC 2.4.1.-)	0.07	-	mit	0					450
P07051 UniProt NPD GO	ROLC_NICGL	Cytokinin-beta-glucosidase (EC 3.2.1.-) (Protein ROL C)	0.07	-	cyt	0					180
Q9U6X1 UniProt NPD GO	ACTP3_RADMG	Cytolysin-3 precursor (Cytolysin III) (HMg III)	0.07	-	exc	0	Secreted protein. Found in nematocyst				211
P97265 UniProt NPD GO	GBA3_CAVPO	Cytosolic beta-glucosidase (EC 3.2.1.21)	0.07	-	cyt	0	Cytoplasm; cytosol				469
Q96KP4 UniProt NPD GO	CNDP2_HUMAN	Cytosolic nonspecific dipeptidase (Glutamate carboxypeptidase-like protein 1) (CNDP dipeptidase 2)	0.07	-	nuc	0					475
P01467 UniProt NPD GO	CX1_NAJMO	Cytotoxin 1 (Cardiotoxin XIIB) (Cytotoxin V-II-1) (CTX IIB)	0.07	-	nuc	0	Secreted protein			2CCX	60
P01474 UniProt NPD GO	CX2_NAJME	Cytotoxin 2 (Cytotoxin V-II-2/V-II-3)	0.07	-	nuc	0	Secreted protein				61
P01470 UniProt NPD GO	CX3_NAJMO	Cytotoxin 3 (Cytotoxin V-II-3)	0.07	-	nuc	0	Secreted protein				60
P42288 UniProt NPD GO	DRD1_DIDMA	D(1A) dopamine receptor	0.07	-	end	7 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...				446
P24552 UniProt NPD GO	OXDA_FUSSO	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.07	-	pox	1 *	Peroxisome (Potential)				361
P18894 UniProt NPD GO	OXDA_MOUSE	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.07	-	nuc	0	Peroxisome				346
P80324 UniProt NPD GO	OXDA_RHOTO	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.07	-	pox	1 *	Peroxisome (Potential)			1C0P	368
Q02337 UniProt NPD GO	BDH_BOVIN	D-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix				344
P80254 UniProt NPD GO	DOPD_RAT	D-dopachrome decarboxylase (EC 4.1.1.84) (D-dopachrome tautomerase)	0.07	-	cyt	0	Cytoplasm				117
O94923 UniProt NPD GO	GLCE_HUMAN	D-glucuronyl C5-epimerase (EC 5.1.3.-) (Heparin/heparan sulfate:glucuronic acid C5 epimerase)	0.07	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi apparatus [ISS]			617
Q754U2 UniProt NPD GO	DAD3_ASHGO	DASH complex subunit DAD3 (Outer kinetochore protein DAD3)	0.07	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				85
P62505 UniProt NPD GO	DAD3_SCHPO	DASH complex subunit dad3 (Outer kinetochore protein dad3)	0.07	-	cyt	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)	DASH complex [IDA]			86
Q9LFN6 UniProt NPD GO	RH56_ARATH	DEAD-box ATP-dependent RNA helicase 56 (EC 3.6.1.-)	0.07	-	cyt	0	Nucleus (By similarity)				427
Q7G7J6 UniProt NPD GO	SLR1_ORYSA	DELLA protein SLR1 (Protein SLENDER RICE1) (Gibberellic acid-insensitive mutant protein) (OsGAI)	0.07	-	cyt	0	Nucleus				625
Q9ZUP2 UniProt NPD GO	RECA3_ARATH	DNA repair protein recA homolog 3 (Recombinase A homolog 3)	0.07	-	cyt	0	Cytoplasm (By similarity)				376
Q12146 UniProt NPD GO	PSF3_YEAST	DNA replication complex GINS protein PSF1 (Partner of Sld five 3)	0.07	-	mit	0	Nucleus	GINS complex [IPI]			194
Q6QN04 UniProt NPD GO	RPB10_CHILA	DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5)	0.07	-	cyt	0	Nucleus				67
P62875 UniProt NPD GO	RPB10_HUMAN	DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5)	0.07	-	cyt	0	Nucleus		601189		67
P62876 UniProt NPD GO	RPB10_MOUSE	DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5)	0.07	-	cyt	0	Nucleus				67
P52435 UniProt NPD GO	RPO2J_HUMAN	DNA-directed RNA polymerase II subunit J (EC 2.7.7.6) (DNA-directed RNA polymerase II 13.3 kDa polyp ...	0.07	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]	604150		117
Q4G347 UniProt NPD GO	RPOA_EMIHU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.07	-	cyt	0	Plastid; chloroplast				309
P81216 UniProt NPD GO	ALL21_HORSE	Dander allergen Equ c 2.0101 (Fragment)	0.07	-	nuc	0	Secreted protein (Potential)				29
P81217 UniProt NPD GO	ALL22_HORSE	Dander allergen Equ c 2.0102 (Fragment)	0.07	-		0	Secreted protein (Potential)				19
Q5G859 UniProt NPD GO	DEF7_PANTR	Defensin 7 precursor (Defensin, alpha 7)	0.07	-	exc	0	Secreted protein				94
Q8LED0 UniProt NPD GO	DDPS7_ARATH	Dehydrodolichyl diphosphate synthase 7 (EC 2.5.1.-) (Dedol-PP synthase 7)	0.07	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				271
Q6UWP2 UniProt NPD GO	DHR11_HUMAN	Dehydrogenase/reductase SDR family member 11 precursor (EC 1.-.-.-)	0.07	-	mit	1 *	Secreted protein (Potential)			1XG5	260
Q8SPU8 UniProt NPD GO	DHRS4_BOVIN	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.07	-	cyt	0	Peroxisome (By similarity)	mitochondrion [ISS]			260
Q8WNV7 UniProt NPD GO	DHRS4_PIG	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.07	-	mit	0	Peroxisome	mitochondrion [ISS]			260
P54887 UniProt NPD GO	P5CS1_ARATH	Delta 1-pyrroline-5-carboxylate synthetase A (P5CS A) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (G ...	0.07	-	nuc	0					717
P36209 UniProt NPD GO	STS1_SCHPO	Delta(24(24(1)))-sterol reductase (EC 1.3.1.71) (Sterol delta(24(28))-reductase) (C-24(28) sterol re ...	0.07	-	vac	8 *	Membrane; multi-pass membrane protein (Probable)				453
Q750E0 UniProt NPD GO	HEM2_ASHGO	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.07	-	cyt	0					340

You are viewing entries 69851 to 69900 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.