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
O13880 UniProt NPD GO	VHT1_SCHPO	Vitamin H transporter 1 (H+/biotin symporter vht1)	0.11	-	end	12	Membrane; multi-pass membrane protein (Potential)	plasma membrane [TAS]			568
P19010 UniProt NPD GO	VITB1_XENLA	Vitellogenin-B1 precursor (VTG B1) (Fragment)	0.11	-	exc	0					71
Q5Q9Z2 UniProt NPD GO	VHL_CANFA	Von Hippel-Lindau disease tumor suppressor (pVHL)	0.11	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Nucleus (By simila ...				219
Q14508 UniProt NPD GO	WFDC2_HUMAN	WAP four-disulfide core domain protein 2 precursor (Major epididymis-specific protein E4) (Epididyma ...	0.11	-	exc	1 *	Secreted protein (Potential)	extracellular space [TAS]			124
Q5ZL16 UniProt NPD GO	WIPI3_CHICK	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.11	-	cyt	0					344
Q9BV38 UniProt NPD GO	WDR18_HUMAN	WD repeat protein 18	0.11	-	nuc	0					432
Q32PJ6 UniProt NPD GO	WDR39_BOVIN	WD repeat protein 39	0.11	-	cyt	0	Nucleus (By similarity)				339
P01173 UniProt NPD GO	WAP_MOUSE	Whey acidic protein precursor (WAP)	0.11	-	exc	0	Secreted protein				134
P43074 UniProt NPD GO	WHS11_CANAL	White colony protein WHS11	0.11	-	nuc	0					65
Q8VCE2 UniProt NPD GO	XAB1_MOUSE	XPA-binding protein 1	0.11	-	cyt	0	Cytoplasm (By similarity)				372
Q8VEH8 UniProt NPD GO	XTP3B_MOUSE	XTP3-transactivated gene B protein homolog precursor	0.11	-	mit	0	Secreted protein (Potential)				483
Q9FV46 UniProt NPD GO	ZDS_TARER	Zeta-carotene desaturase, chloroplast precursor (EC 1.14.99.30) (Carotene 7,8-desaturase)	0.11	-	mit	0	Plastid; chloroplast. Plastid; chromoplast				587
Q9NXT0 UniProt NPD GO	ZN586_HUMAN	Zinc finger protein 586	0.11	-	nuc	0	Nucleus (Probable)				252
O14863 UniProt NPD GO	ZNT4_HUMAN	Zinc transporter 4 (ZnT-4) (Solute carrier family 30 member 4)	0.11	-	end	6	Endosome; endosomal membrane; multi-pass membrane protein (Probable)		602095		429
Q9PUB8 UniProt NPD GO	KE4_BRARE	Zinc transporter Slc39a7 (Solute carrier family 39 member 7) (Histidine-rich membrane protein Ke4) ( ...	0.11	-	end	4	Membrane; multi-pass membrane protein (Probable)				352
Q9D856 UniProt NPD GO	S39A5_MOUSE	Zinc transporter ZIP5 precursor (Solute carrier family 39 member 5)	0.11	-	end	6	Cell membrane; basolateral cell membrane; multi-pass membrane protein	basolateral plasma membrane [IDA]			535
Q63678 UniProt NPD GO	ZA2G_RAT	Zinc-alpha-2-glycoprotein precursor (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP)	0.11	-	mit	0	Secreted protein	extracellular region [ISS] extracellular space [TAS]			296
Q71U53 UniProt NPD GO	IPKA_PIG	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha)	0.11	-	nuc	0					75
P61925 UniProt NPD GO	IPKA_HUMAN	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha) (cAMP-dependent protein kinase inhibitor, ...	0.11	-	nuc	0			606059	2C1B	75
P61926 UniProt NPD GO	IPKA_RABIT	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha) (cAMP-dependent protein kinase inhibitor, ...	0.11	-	nuc	0				2ERZ	75
P27775 UniProt NPD GO	IPKB_RAT	cAMP-dependent protein kinase inhibitor beta (PKI-beta) (cAMP-dependent protein kinase inhibitor, te ...	0.11	-	nuc	0					70
O70139 UniProt NPD GO	IPKG_MOUSE	cAMP-dependent protein kinase inhibitor gamma (PKI-gamma)	0.11	-	nuc	0					76
Q7YQJ4 UniProt NPD GO	IPKG_PIG	cAMP-dependent protein kinase inhibitor gamma (PKI-gamma)	0.11	-	nuc	0					76
P68180 UniProt NPD GO	KAPCB_CRIGR	cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.11.11) (PKA C-beta)	0.11	-	nuc	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cAMP-dependent protein kinase complex [ISS]			350
P22694 UniProt NPD GO	KAPCB_HUMAN	cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.11.11) (PKA C-beta)	0.11	-	nuc	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cAMP-dependent protein kinase complex [TAS]	176892		350
P68181 UniProt NPD GO	KAPCB_MOUSE	cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.11.11) (PKA C-beta)	0.11	-	nuc	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cAMP-dependent protein kinase complex [TAS]			350
P68182 UniProt NPD GO	KAPCB_RAT	cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.11.11) (PKA C-beta)	0.11	-	nuc	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cAMP-dependent protein kinase complex [ISS]			350
Q759Y8 UniProt NPD GO	SEN15_ASHGO	tRNA-splicing endonuclease subunit SEN15 (tRNA-intron endonuclease SEN15)	0.11	-	cyt	0					118
Q9M1E8 UniProt NPD GO	SEN21_ARATH	tRNA-splicing endonuclease subunit Sen2-1 (EC 3.1.27.9) (AtSen1) (tRNA-intron endonuclease Sen2-1)	0.11	-	cyt	0	Nucleus (By similarity)				237
Q8VEB4 UniProt NPD GO	LYPA3_MOUSE	1-O-acylceramide synthase precursor (EC 2.3.1.-) (ACS) (Lysosomal phospholipase A2) (Lysophospholipa ...	0.10	-	mit	1 *	Secreted protein (By similarity). Lysosome	soluble fraction [IDA]			412
Q42868 UniProt NPD GO	PLSC_LIMAL	1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) (1-AGP acyltransferase) (1-AGPAT) (Lyso ...	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				281
Q42870 UniProt NPD GO	PLSC_LIMDO	1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) (1-AGP acyltransferase) (1-AGPAT) (Lyso ...	0.10	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				281
Q8K2C8 UniProt NPD GO	PLCF_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase zeta precursor (EC 2.3.1.51) (1-AGP acyltransferase 6 ...	0.10	-	vac	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] integral to endoplasmic reticulum membrane [NAS]			456
Q9M6E2 UniProt NPD GO	DBAT_TAXCU	10-deacetylbaccatin III 10-O-acetyltransferase (EC 2.3.1.167) (DBAT)	0.10	-	cyt	0					440
Q9XG54 UniProt NPD GO	OPR1_LYCES	12-oxophytodienoate reductase 1 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 1) (OPDA-reductas ...	0.10	-	cyt	0	Cytoplasm			1ICS	376
Q7M1I4 UniProt NPD GO	CWP04_PHAVU	136 kDa hydroxyproline-rich cell wall glycoprotein, major component (Fragment)	0.10	-	nuc	0	Cell wall				30
P93213 UniProt NPD GO	14338_LYCES	14-3-3 protein 8	0.10	-	cyt	0					261
Q01544 UniProt NPD GO	HSP21_IPONI	17.2 kDa class II heat shock protein	0.10	-	cyt	0	Cytoplasm (By similarity)				155
P62368 UniProt NPD GO	ISPF_PLAF7	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase precursor (EC 4.6.1.12) (MECPS) (MECDP-synthas ...	0.10	-	mit	1 *					240
P62369 UniProt NPD GO	ISPF_PLAFX	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase precursor (EC 4.6.1.12) (MECPS) (MECDP-synthas ...	0.10	-	mit	1 *					240
Q9CAK8 UniProt NPD GO	ISPF_ARATH	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplast precursor (EC 4.6.1.12) (MECPS) ( ...	0.10	-	nuc	0	Plastid; chloroplast				231
P29257 UniProt NPD GO	LEC2_CYTSC	2-acetamido-2-deoxy-D-galactose-binding seed lectin 2 (2-acetamido-2-deoxy-D-galactose-binding seed ...	0.10	-	nuc	0					248
Q9QXE0 UniProt NPD GO	HPCL_MOUSE	2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-) (2-HPCL)	0.10	-	mit	0	Peroxisome (By similarity)	peroxisome [ISS]			581
O04974 UniProt NPD GO	LEU1B_LYCPN	2-isopropylmalate synthase B (EC 2.3.3.13) (Alpha-isopropylmalate synthase B) (Alpha-IPM synthetase ...	0.10	-	mit	0					612
P15845 UniProt NPD GO	SM20_SCHMA	20 kDa calcium-binding protein (Antigen SM20)	0.10	-	cyt	0	Tegument; tegumental membrane. Associated with the tegumental membrane				154
P09226 UniProt NPD GO	CB25_TETTH	25 kDa calcium-binding protein (TCBP-25) [Contains: 10 kDa calcium-binding protein (TCBP-10)]	0.10	-	cyt	0					218
P13401 UniProt NPD GO	OS25_PLAGA	25 kDa ookinete surface antigen precursor (Pgs25)	0.10	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				215
P62194 UniProt NPD GO	PRS8_BOVIN	26S protease regulatory subunit 8 (Proteasome subunit p45) (p45/SUG) (Proteasome 26S subunit ATPase ...	0.10	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [ISS] nucleus [ISS] proteasome complex (sensu Eukaryota) [ISS]			406
P62197 UniProt NPD GO	PRS8_PIG	26S protease regulatory subunit 8 (Proteasome subunit p45) (p45/SUG) (Proteasome 26S subunit ATPase ...	0.10	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [ISS] nucleus [ISS] proteasome complex (sensu Eukaryota) [ISS]			406
P62195 UniProt NPD GO	PRS8_HUMAN	26S protease regulatory subunit 8 (Proteasome subunit p45) (p45/SUG) (Proteasome 26S subunit ATPase ...	0.10	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA] proteasome complex (sensu Eukaryota) [IDA]	601681		406

You are viewing entries 63751 to 63800 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.