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
Q9P2V4 UniProt NPD GO	LRC21_HUMAN	Leucine-rich repeat-containing protein 21 precursor (Photoreceptor-associated LRR superfamily protei ...	0.27	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	integral to endoplasmic reticulum membrane [ISS]			623
P59034 UniProt NPD GO	LRRC3_MOUSE	Leucine-rich repeat-containing protein 3 precursor	0.27	-	exc	1					257
Q9BV99 UniProt NPD GO	LRC61_HUMAN	Leucine-rich repeat-containing protein 61	0.27	-	nuc	0					259
Q5S7W5 UniProt NPD GO	NTAL_CHICK	Linker for activation of T-cells family member 2 (Non-T-cell activation linker) (Linker for activati ...	0.27	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts (By similarity)				198
Q6XZB0 UniProt NPD GO	LIPI_HUMAN	Lipase member I precursor (EC 3.1.1.-) (Membrane-associated phosphatidic acid-selective phospholipas ...	0.27	-	end	0	Secreted protein (Potential). May associate with lipid draft		609252		460
Q99JY8 UniProt NPD GO	LPP3_MOUSE	Lipid phosphate phosphohydrolase 3 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2b) (Phosphatidate ph ...	0.27	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				312
O14495 UniProt NPD GO	LPP3_HUMAN	Lipid phosphate phosphohydrolase 3 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2b) (Phosphatidate ph ...	0.27	-	end	6 *	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein. Cel ...	membrane [TAS]	607125		311
Q76I22 UniProt NPD GO	LOX1_ORYSA	Lipoxygenase 1 (EC 1.13.11.12) (9-lipoxygenase) (r9-LOX1)	0.27	-	nuc	0	Cytoplasm (By similarity)				863
O00534 UniProt NPD GO	LHR2A_HUMAN	Loss of heterozygosity 11 chromosomal region 2 gene A protein (Breast cancer suppressor candidate 1) ...	0.27	-	cyt	0			602929		786
Q8BP40 UniProt NPD GO	PPA6_MOUSE	Lysophosphatidic acid phosphatase type 6 precursor (EC 3.1.3.2) (Acid phosphatase 6, lysophosphatidi ...	0.27	-	mit	0	Secreted protein (By similarity)				418
Q9UWF6 UniProt NPD GO	PLB1_CANAL	Lysophospholipase 1 precursor (EC 3.1.1.5) (Phospholipase B 1) (CaPLB1)	0.27	-	nuc	0	Secreted protein (Probable)				605
P49129 UniProt NPD GO	LAMP1_CRIGR	Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) (Lysosomal membrane glycoprotein A) ( ...	0.27	-	exc	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Endosome; endosomal membrane; si ...				407
Q924C6 UniProt NPD GO	LOXL4_MOUSE	Lysyl oxidase homolog 4 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 4) (Lysyl oxidase-related ...	0.27	-	exc	0	Secreted protein; extracellular space (Potential)	extracellular region [IDA]			757
Q9QXT0 UniProt NPD GO	MSAP_MOUSE	MIR-interacting saposin-like protein precursor (Transmembrane protein 4) (Putative secreted protein ...	0.27	-	end	0					182
P30204 UniProt NPD GO	MSRE_MOUSE	Macrophage scavenger receptor types I and II (Macrophage acetylated LDL receptor I and II) (Scavenge ...	0.27	-	nuc	1	Membrane; single-pass type II membrane protein				458
Q5ZMI4 UniProt NPD GO	MVP_CHICK	Major vault protein (MVP)	0.27	-	cyt	0	Cytoplasm (By similarity)				849
P30952 UniProt NPD GO	MASY_YEAST	Malate synthase 1, glyoxysomal (EC 2.3.3.9)	0.27	-	pox	0	Glyoxysome	cytoplasm [IDA]			554
Q5RAV8 UniProt NPD GO	M6PBP_PONPY	Mannose-6-phosphate receptor-binding protein 1	0.27	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). Membrane associated on endosomes. Detected in t ...				434
P53008 UniProt NPD GO	CWH41_YEAST	Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Processing A-glucosidase I) (Glucosidase I)	0.27	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum membrane [IDA]			833
Q08156 UniProt NPD GO	KIT_CHICK	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.27	-	mit	2	Membrane; single-pass type I membrane protein				960
Q02593 UniProt NPD GO	BAP12_SCHCO	Mating-type pheromone BAP1(2) precursor	0.27	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				48
Q10739 UniProt NPD GO	MMP14_RAT	Matrix metalloproteinase-14 precursor (EC 3.4.24.80) (MMP-14) (Membrane-type matrix metalloproteinas ...	0.27	-	end	1	Membrane; single-pass type I membrane protein (Potential)				582
Q99542 UniProt NPD GO	MMP19_HUMAN	Matrix metalloproteinase-19 precursor (EC 3.4.24.-) (MMP-19) (Matrix metalloproteinase RASI) (MMP-18 ...	0.27	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [NAS]	601807		508
O18767 UniProt NPD GO	MMP20_BOVIN	Matrix metalloproteinase-20 precursor (EC 3.4.24.-) (MMP-20) (Enamel metalloproteinase) (Enamelysin) ...	0.27	-	exc	0	Secreted protein; extracellular space; extracellular matrix				481
Q13503 UniProt NPD GO	MED21_HUMAN	Mediator of RNA polymerase II transcription subunit 21 (RNA polymerase II holoenzyme component SRB7) ...	0.27	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase II, core complex [TAS] mediator complex [IDA]	603800		144
Q8HXY8 UniProt NPD GO	ACADM_MACFA	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.27	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial matrix [ISS] mitochondrion [ISS]			421
Q5YKK9 UniProt NPD GO	OPN4_FELCA	Melanopsin (Opsin-4)	0.27	-	end	6	Membrane; multi-pass membrane protein. Found in soma, dendrites and proximal part of axons of certai ...				487
P81546 UniProt NPD GO	TIMP1_CANFA	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.27	-	nuc	0	Secreted protein				207
P20414 UniProt NPD GO	TIMP1_BOVIN	Metalloproteinase inhibitor 1 precursor (TIMP-1) (Embryogenin-1) (EG-1)	0.27	-	exc	0	Secreted protein				207
Q68FL6 UniProt NPD GO	SYM_MOUSE	Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.27	-	mit	0	Cytoplasm (Probable)				902
Q9LDD8 UniProt NPD GO	MCCB_ARATH	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.4) (3-Methylcrotonyl-C ...	0.27	+	mit	0	Mitochondrion; mitochondrial matrix				587
Q8TCB7 UniProt NPD GO	METL6_HUMAN	Methyltransferase-like protein 6 (EC 2.1.1.-)	0.27	-	mit	0					255
Q9UPY8 UniProt NPD GO	MARE3_HUMAN	Microtubule-associated protein RP/EB family member 3 (End-binding protein 3) (EB3) (EB1 protein fami ...	0.27	-	cyt	0	Cytoplasm. Associated with the microtubule network		605788	1WYO	281
Q6PER3 UniProt NPD GO	MARE3_MOUSE	Microtubule-associated protein RP/EB family member 3 (End-binding protein 3) (EB3) (EB1 protein fami ...	0.27	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				281
Q5XIT1 UniProt NPD GO	MARE3_RAT	Microtubule-associated protein RP/EB family member 3 (End-binding protein 3) (EB3) (EB1 protein fami ...	0.27	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				281
Q6TS35 UniProt NPD GO	TAU_SPECI	Microtubule-associated protein tau	0.27	-	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Mostly found in the axons of neur ...				429
Q9W6H0 UniProt NPD GO	MIME_CHICK	Mimecan precursor (Osteoglycin)	0.27	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				294
Q503X2 UniProt NPD GO	RM04_BRARE	Mitochondrial 39S ribosomal protein L4 (L4mt) (MRP-L4)	0.27	-	mit	0	Mitochondrion (By similarity)				302
Q9BYD3 UniProt NPD GO	RM04_HUMAN	Mitochondrial 39S ribosomal protein L4 (L4mt) (MRP-L4)	0.27	-	mit	0	Mitochondrion				311
Q9DCU6 UniProt NPD GO	RM04_MOUSE	Mitochondrial 39S ribosomal protein L4 (L4mt) (MRP-L4)	0.27	-	mit	0	Mitochondrion (By similarity)				294
P18496 UniProt NPD GO	ATP10_YEAST	Mitochondrial ATPase complex subunit ATP10	0.27	-	mit	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial envelope [IPI]			279
Q6FK91 UniProt NPD GO	MG101_CANGA	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.27	-	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				244
P47045 UniProt NPD GO	TIM54_YEAST	Mitochondrial import inner membrane translocase subunit TIM54	0.27	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein. Import into inner membran ...	mitochondrial inner membrane protein insert... [IDA]			478
Q3ZBS8 UniProt NPD GO	TIM8A_BOVIN	Mitochondrial import inner membrane translocase subunit Tim8 A	0.27	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				97
Q9WVA2 UniProt NPD GO	TIM8A_MOUSE	Mitochondrial import inner membrane translocase subunit Tim8 A (Deafness dystonia protein 1 homolog) ...	0.27	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	mitochondrion [IDA]			97
Q9XGX9 UniProt NPD GO	TIM9_ARATH	Mitochondrial import inner membrane translocase subunit Tim9	0.27	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
Q616Q2 UniProt NPD GO	TIM8_CAEBR	Mitochondrial import inner membrane translocase subunit tim-8	0.27	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				83
P26869 UniProt NPD GO	RT10_MARPO	Mitochondrial ribosomal protein S10	0.27	-	mit	0	Mitochondrion				102
P46747 UniProt NPD GO	RT13_PROWI	Mitochondrial ribosomal protein S13	0.27	-	nuc	0	Mitochondrion				119
P46741 UniProt NPD GO	RT02_PROWI	Mitochondrial ribosomal protein S2	0.27	-	nuc	0	Mitochondrion				274

You are viewing entries 43351 to 43400 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.