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
P27049 UniProt NPD GO	BTG2_RAT	BTG2 protein (NGF-inducible anti-proliferative protein PC3)	0.21	-	nuc	0					158
P23562 UniProt NPD GO	B3AT_RAT	Band 3 anion transport protein (Anion exchange protein 1) (AE 1) (Solute carrier family 4 member 1) ...	0.21	-	end	10	Cell membrane; basolateral cell membrane; multi-pass membrane protein. In the basolateral membrane o ...				927
P19141 UniProt NPD GO	CRBB3_BOVIN	Beta crystallin B3 (Beta-B3-crystallin)	0.21	-	cyt	0					210
Q9N293 UniProt NPD GO	B3GT5_GORGO	Beta-1,3-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,3-GalTase 5) (Beta3Gal-T5) (b3Gal-T5) (UDP-gal ...	0.21	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				298
Q9JI67 UniProt NPD GO	B3GT5_MOUSE	Beta-1,3-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,3-GalTase 5) (Beta3Gal-T5) (b3Gal-T5) (UDP-gal ...	0.21	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				308
Q00973 UniProt NPD GO	B4GN1_HUMAN	Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92) ((N-acetylneuraminyl)-galactosylglucosylc ...	0.21	-	vac	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	membrane fraction [TAS]	601873		533
P15535 UniProt NPD GO	B4GT1_MOUSE	Beta-1,4-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,4-GalTase 1) (Beta4Gal-T1) (b4Gal-T1) (UDP-gal ...	0.21	-	mit	1 *	Isoform Long, isoform Short: Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II ...	Golgi apparatus [IDA] plasma membrane [IDA]			399
Q9JMK0 UniProt NPD GO	B4GT5_MOUSE	Beta-1,4-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,4-GalTase 5) (Beta4Gal-T5) (b4Gal-T5) (UDP-gal ...	0.21	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				388
Q91854 UniProt NPD GO	TRCB_XENLA	Beta-TrCP (Beta-transducin repeat-containing protein)	0.21	-	cyt	0					518
P32121 UniProt NPD GO	ARRB2_HUMAN	Beta-arrestin-2 (Arrestin, beta 2)	0.21	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [TAS] plasma membrane [TAS]	107941		409
P02666 UniProt NPD GO	CASB_BOVIN	Beta-casein precursor	0.21	-	exc	0	Secreted protein				224
P10598 UniProt NPD GO	CASB_MOUSE	Beta-casein precursor	0.21	-	exc	0	Secreted protein				231
Q5IAA6 UniProt NPD GO	D108B_PANTR	Beta-defensin 108B precursor (Defensin, beta 108B) (Defensin, beta 108) (Beta-defensin 8) (DEFB-8) ( ...	0.21	-	nuc	0	Secreted protein (By similarity)				53
Q30KL4 UniProt NPD GO	DB113_PANTR	Beta-defensin 113 precursor (Defensin, beta 113)	0.21	-	exc	0	Secreted protein (By similarity)				82
P46160 UniProt NPD GO	BD02_BOVIN	Beta-defensin 2 (BNDB-2) (BNBD-2)	0.21	-	mit	0	Secreted protein				40
Q8BGW9 UniProt NPD GO	BD29_MOUSE	Beta-defensin 29 precursor (Defensin, beta 29) (BD-29) (mBD-29)	0.21	-	vac	1 *	Secreted protein (By similarity)				78
Q39692 UniProt NPD GO	INV2_DAUCA	Beta-fructofuranosidase, insoluble isoenzyme 2 precursor (EC 3.2.1.26) (Sucrose hydrolase 2) (Invert ...	0.21	-	mit	1 *	Cell wall. Ionically bound to the cell wall				592
Q56UD3 UniProt NPD GO	INV3_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 3 precursor (EC 3.2.1.26) (Sucrose hydrolase 3) (Invert ...	0.21	+	mit	1 *	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				586
P81446 UniProt NPD GO	ML1_VISAL	Beta-galactoside-specific lectin 1 precursor (Beta-galactoside-specific lectin I) (Viscumin) [Contai ...	0.21	-	mit	0				1PUU	531
Q9Y8G7 UniProt NPD GO	C505_FUSOX	Bifunctional P-450:NADPH-P450 reductase (Fatty acid omega-hydroxylase) (P450foxy) [Includes: Cytochr ...	0.21	-	cyt	0	Membrane; peripheral membrane protein				1066
P13922 UniProt NPD GO	DRTS_PLAFK	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.21	-	cyt	0				1J3K	608
P56380 UniProt NPD GO	AP4A_MOUSE	Bis(5'-nucleosyl)-tetraphosphatase [Asymmetrical] (EC 3.6.1.17) (Diadenosine 5',5'''-P1,P4-tetraphos ...	0.21	-	mit	0					146
Q6PEC0 UniProt NPD GO	AP4A_RAT	Bis(5'-nucleosyl)-tetraphosphatase [Asymmetrical] (EC 3.6.1.17) (Diadenosine 5',5'''-P1,P4-tetraphos ...	0.21	-	mit	0					146
Q10589 UniProt NPD GO	BST2_HUMAN	Bone marrow stromal antigen 2 (BST-2) (CD317 antigen)	0.21	-	end	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	600534		180
P13839 UniProt NPD GO	SIAL_RAT	Bone sialoprotein-2 precursor (Bone sialoprotein II) (BSP II) (Cell-binding sialoprotein) (Integrin- ...	0.21	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]			320
P20293 UniProt NPD GO	BRAC_MOUSE	Brachyury protein (T protein)	0.21	-	nuc	0	Nucleus				436
P70658 UniProt NPD GO	CXCR4_MOUSE	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (Stromal cell-derived factor 1 receptor) (SDF-1 re ...	0.21	-	end	7 *	Membrane; multi-pass membrane protein	growth cone [IDA]			359
P56545 UniProt NPD GO	CTBP2_HUMAN	C-terminal-binding protein 2 (CtBP2)	0.21	+	nuc	0	Nucleus (Potential)		602619		445
Q9QZ15 UniProt NPD GO	CLC4A_MOUSE	C-type lectin domain family 4 member A (C-type lectin superfamily member 6) (Dendritic cell immunore ...	0.21	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)	membrane fraction [TAS]			238
O88875 UniProt NPD GO	BY55_MOUSE	CD160 antigen precursor (Natural killer cell receptor BY55)	0.21	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				185
Q9BH13 UniProt NPD GO	CD166_BOVIN	CD166 antigen precursor (Activated leukocyte-cell adhesion molecule) (ALCAM)	0.21	+	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				583
Q03323 UniProt NPD GO	SDC1_YEAST	COMPASS component SDC1 (Complex proteins associated with SET1 protein SDC1) (Set1C component SDC1) ( ...	0.21	-	nuc	0	Nucleus (Probable)	COMPASS complex [IPI]			175
P68353 UniProt NPD GO	CSN2_BRAOL	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (FUSCA protein 12) (FUSCA12) (Fragments)	0.21	-	nuc	0	Cytoplasm. Nucleus				39
Q9UT51 UniProt NPD GO	CSN3_SCHPO	COP9 signalosome complex subunit 3 (CSN complex subunit 3) (SGN3)	0.21	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				334
P68359 UniProt NPD GO	CSN4_BRAOL	COP9 signalosome complex subunit 4 (Signalosome subunit 4) (Constitutive photomorphogenesis protein ...	0.21	-	nuc	0	Cytoplasm. Nucleus				45
Q4WZP2 UniProt NPD GO	CSN5_ASPFU	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.21	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				334
Q96NX5 UniProt NPD GO	KCC1G_HUMAN	Calcium/calmodulin-dependent protein kinase type 1G (EC 2.7.11.17) (CaM kinase IG) (CaM kinase I gam ...	0.21	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similari ...				476
Q9UQM7 UniProt NPD GO	KCC2A_HUMAN	Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.11.17) (CaM-kinase II alpha ...	0.21	-	mit	0			114078		478
P11275 UniProt NPD GO	KCC2A_RAT	Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.11.17) (CaM-kinase II alpha ...	0.21	-	mit	0		calcium- and calmodulin-dependent protein k... [TAS] dendrite [IDA]			478
Q32L92 UniProt NPD GO	CNN3_BOVIN	Calponin-3 (Calponin, acidic isoform)	0.21	-	nuc	0					329
Q15417 UniProt NPD GO	CNN3_HUMAN	Calponin-3 (Calponin, acidic isoform)	0.21	-	nuc	0			602374		329
P23280 UniProt NPD GO	CAH6_HUMAN	Carbonic anhydrase 6 precursor (EC 4.2.1.1) (Carbonic anhydrase VI) (Carbonate dehydratase VI) (CA-V ...	0.21	-	exc	0	Secreted protein		114780		308
Q8BX07 UniProt NPD GO	CTDS2_MOUSE	Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 (EC 3.1.3.16)	0.21	-	cyt	0	Nucleus (Potential)				270
P00730 UniProt NPD GO	CBPA1_BOVIN	Carboxypeptidase A1 precursor (EC 3.4.17.1)	0.21	-	exc	0	Secreted protein			8CPA	419
Q9EQV9 UniProt NPD GO	CBPB2_RAT	Carboxypeptidase B2 precursor (EC 3.4.17.20) (Carboxypeptidase U) (Thrombin-activable fibrinolysis i ...	0.21	-	cyt	0	Secreted protein				422
P26678 UniProt NPD GO	PPLA_HUMAN	Cardiac phospholamban (PLB)	0.21	-	mit	1 *	Membrane		172405	1ZLL	52
P61014 UniProt NPD GO	PPLA_MOUSE	Cardiac phospholamban (PLB)	0.21	-	mit	1 *	Membrane (By similarity)				52
P61015 UniProt NPD GO	PPLA_RABIT	Cardiac phospholamban (PLB)	0.21	-	mit	1 *	Membrane			1N7L	52
P61016 UniProt NPD GO	PPLA_RAT	Cardiac phospholamban (PLB)	0.21	-	mit	1 *	Membrane				52
Q9M9Y8 UniProt NPD GO	CRTSO_ARATH	Carotenoid isomerase, chloroplast precursor (EC 5.-.-.-) (CrtISO) (Carotenoid and chloroplast regula ...	0.21	-	nuc	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (By similarity)				587

You are viewing entries 49251 to 49300 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.