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
Q08956 UniProt NPD GO	YIG1_YEAST	Protein YIG1	0.26	-	cyt	0	Cytoplasm. Nucleus	cytosol [IDA] nucleus [IDA]			461
P46508 UniProt NPD GO	YME1_SCHMA	Protein YME1 homolog (EC 3.4.24.-)	0.26	-	mit	1					662
Q5RDA8 UniProt NPD GO	ZPI_PONPY	Protein Z-dependent protease inhibitor precursor (PZ-dependent protease inhibitor) (PZI) (Serpin A10 ...	0.26	-	vac	0	Secreted protein (By similarity)				443
Q9U5V3 UniProt NPD GO	U239_DROSI	Protein anon-73B1	0.26	+	nuc	1 *		integral to membrane [NAS]			87
P56674 UniProt NPD GO	HH_DROHY	Protein hedgehog precursor [Contains: Protein hedgehog N-product (Hh-Np) (N-Hh); Protein hedgehog C- ...	0.26	-	exc	0	Protein hedgehog: Secreted protein (By similarity). Cell surface (By similarity). Protein hedgehog N ...				422
P31506 UniProt NPD GO	HUNB_CALVI	Protein hunchback (Fragment)	0.26	-	nuc	0	Nucleus (Probable)				54
Q9HAT8 UniProt NPD GO	PELI2_HUMAN	Protein pellino homolog 2 (Pellino-2)	0.26	-	cyt	0					420
P49444 UniProt NPD GO	PP2C_PARTE	Protein phosphatase 2C (EC 3.1.3.16) (PP2C)	0.26	-	cyt	0	Membrane; peripheral membrane protein				300
Q09826 UniProt NPD GO	SDS23_SCHPO	Protein sds23/moc1 (Phosphoprotein at stationary phase 1 protein)	0.26	-	nuc	0	Cytoplasm	cell tip [IDA]			408
P79060 UniProt NPD GO	SUI1_SCHPO	Protein translation factor sui1	0.26	-	cyt	0					109
P22804 UniProt NPD GO	BET1_YEAST	Protein transport protein BET1 (Suppressor of loss of YPT1 protein 12) (Protein SLY12)	0.26	-	cyt	1	Membrane; single-pass type IV membrane protein (Probable)	endoplasmic reticulum membrane [IDA] ER to Golgi transport vesicle [IDA]			142
Q09730 UniProt NPD GO	SFT1_SCHPO	Protein transport protein sft1	0.26	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				91
Q99041 UniProt NPD GO	TGM4_RAT	Protein-glutamine gamma-glutamyltransferase 4 (EC 2.3.2.13) (Transglutaminase-4) (TGase-4) (Dorsal p ...	0.26	-	cyt	0	Secreted protein				668
Q9D7I9 UniProt NPD GO	TGM5_MOUSE	Protein-glutamine gamma-glutamyltransferase 5 (EC 2.3.2.13) (Transglutaminase-5) (TGase 5)	0.26	-	end	0	Cytoplasm (By similarity). Associated with intermediate filaments (By similarity)				723
Q9Y5I3 UniProt NPD GO	PCDA1_HUMAN	Protocadherin alpha 1 precursor (PCDH-alpha1)	0.26	+	nuc	0	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted p ...	integral to plasma membrane [TAS]	606307		950
Q5DRE8 UniProt NPD GO	PCDA4_PANTR	Protocadherin alpha 4 precursor (PCDH-alpha4)	0.26	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				947
Q9UN72 UniProt NPD GO	PCDA7_HUMAN	Protocadherin alpha 7 precursor (PCDH-alpha7)	0.26	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606313		937
Q9Y5H6 UniProt NPD GO	PCDA8_HUMAN	Protocadherin alpha 8 precursor (PCDH-alpha8)	0.26	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606314		950
Q5DRE4 UniProt NPD GO	PCDA8_PANTR	Protocadherin alpha 8 precursor (PCDH-alpha8)	0.26	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				950
Q9Y5H3 UniProt NPD GO	PCDGA_HUMAN	Protocadherin gamma A10 precursor (PCDH-gamma-A10)	0.26	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606297		936
Q5DRC1 UniProt NPD GO	PCDGA_PANTR	Protocadherin gamma A10 precursor (PCDH-gamma-A10)	0.26	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				936
Q5DRB9 UniProt NPD GO	PCDGC_PANTR	Protocadherin gamma A12 precursor (PCDH-gamma-A12)	0.26	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				932
Q5DRB8 UniProt NPD GO	PCDG2_PANTR	Protocadherin gamma A2 precursor (PCDH-gamma-A2)	0.26	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				932
O22254 UniProt NPD GO	RL181_ARATH	Putative 60S ribosomal protein L18-1	0.26	-	cyt	0					188
O88696 UniProt NPD GO	CLPP_MOUSE	Putative ATP-dependent Clp protease proteolytic subunit, mitochondrial precursor (EC 3.4.21.92) (End ...	0.26	-	mit	0		mitochondrion [IDA]			272
Q10233 UniProt NPD GO	RPC2_SCHPO	Putative DNA-directed RNA polymerase III 130 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subuni ...	0.26	-	nuc	0	Nucleus (Potential)				1165
Q18014 UniProt NPD GO	OFUT1_CAEEL	Putative GDP-fucose protein O-fucosyltransferase 1 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransf ...	0.26	-	exc	0	Endoplasmic reticulum (By similarity)	integral to Golgi membrane [ISS]			389
P0C041 UniProt NPD GO	ATL4H_ARATH	Putative RING-H2 finger protein ATL4H	0.26	-	nuc	1					336
Q99388 UniProt NPD GO	S100R_MOUSE	Putative Sp100-related protein	0.26	-	nuc	1					208
Q96HN2 UniProt NPD GO	SAHH3_HUMAN	Putative adenosylhomocysteinase 3 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 3) (AdoHcyase 3) ...	0.26	-	cyt	0					611
Q68FL4 UniProt NPD GO	SAHH3_MOUSE	Putative adenosylhomocysteinase 3 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 3) (AdoHcyase 3) ...	0.26	-	cyt	0					613
Q9LIK7 UniProt NPD GO	ACA13_ARATH	Putative calcium-transporting ATPase 13, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 13 ...	0.26	-	end	8	Membrane; multi-pass membrane protein				1017
Q9C9X5 UniProt NPD GO	CAP12_ARATH	Putative clathrin assembly protein At1g68110	0.26	-	mit	0					379
Q60PP8 UniProt NPD GO	CPLX1_CAEBR	Putative complexin-1	0.26	-	cyt	0	Cytoplasm; cytosol (By similarity)				143
Q21184 UniProt NPD GO	CO155_CAEEL	Putative cuticle collagen 155	0.26	-	nuc	0					266
Q9C8T9 UniProt NPD GO	DRL19_ARATH	Putative disease resistance protein At1g63350	0.26	-	cyt	0					898
Q6BIB1 UniProt NPD GO	CCPR2_DEBHA	Putative heme-binding peroxidase (EC 1.11.1.-)	0.26	-	nuc	0					428
Q9LFF6 UniProt NPD GO	H2B8_ARATH	Putative histone H2B.8 (HTB6)	0.26	-	nuc	0	Nucleus (By similarity)				137
Q6L3Z4 UniProt NPD GO	R1B12_SOLDE	Putative late blight resistance protein homolog R1B-12	0.26	-	nuc	0	Cytoplasm (By similarity)				1296
O13857 UniProt NPD GO	PLB2_SCHPO	Putative lysophospholipase C1A6.03c precursor (EC 3.1.1.5) (Phospholipase B)	0.26	-	cyt	0	Secreted protein (Probable)				624
P53937 UniProt NPD GO	YNI1_YEAST	Putative mitochondrial 40S ribosomal protein YNL081C	0.26	-	nuc	0	Mitochondrion (Potential)	cytoplasm [IDA]			143
Q5JWF8 UniProt NPD GO	CT134_HUMAN	Putative uncharacterized protein C20orf134 precursor	0.26	-	mit	0	Secreted protein (Potential)				245
Q8N813 UniProt NPD GO	CC056_HUMAN	Putative uncharacterized protein C3orf56	0.26	-	nuc	0					242
P43552 UniProt NPD GO	YFF1_YEAST	Putative uncharacterized protein YFL051C precursor	0.26	-	exc	2 *					160
O13534 UniProt NPD GO	YH1A_YEAST	Putative uncharacterized protein YHR214W-A	0.26	-	nuc	0					161
P40442 UniProt NPD GO	YIQ9_YEAST	Putative uncharacterized protein YIL169C precursor	0.26	-	exc	0					995
Q43117 UniProt NPD GO	KPYA_RICCO	Pyruvate kinase isozyme A, chloroplast precursor (EC 2.7.1.40)	0.26	-	mit	0	Plastid; chloroplast				583
Q39734 UniProt NPD GO	PPDK_FLABR	Pyruvate, phosphate dikinase, chloroplast precursor (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase) ...	0.26	-	cyt	0	Plastid; chloroplast				955
O14001 UniProt NPD GO	PVG2_SCHPO	Pyruvylated Gal-beta-1,3-epitope synthesis protein 2 (PvGal synthesis protein 2)	0.26	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	cell tip [IDA]			389
Q22038 UniProt NPD GO	RHOA_CAEEL	RAS-like GTP-binding protein RhoA	0.26	-	cyt	0	Membrane. Cytoplasm. Associated with the membrane and the cytoskeleton throughout development				192

You are viewing entries 44601 to 44650 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.