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
Q9N2C1 UniProt NPD GO	LEP_FELCA	Leptin precursor (Obesity factor)	0.29	-	exc	0	Secreted protein (Probable)				167
Q706D1 UniProt NPD GO	LEP_PHOVI	Leptin precursor (Obesity factor)	0.29	-	exc	0	Secreted protein (Probable)				167
Q5AQJ2 UniProt NPD GO	LCMT1_EMENI	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.29	-	mit	0					382
Q4ICG8 UniProt NPD GO	LCMT1_GIBZE	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.29	+	nuc	0					375
Q8N135 UniProt NPD GO	LGI4_HUMAN	Leucine-rich repeat LGI family member 4 precursor (Leucine-rich glioma-inactivated protein 4) (LGI1- ...	0.29	-	end	0	Secreted protein (Potential)		608303		537
Q96PB8 UniProt NPD GO	LRC3B_HUMAN	Leucine-rich repeat-containing protein 3B precursor (Leucine-rich repeat protein LRP15)	0.29	-	end	1 *					259
Q66JT1 UniProt NPD GO	LRC8E_MOUSE	Leucine-rich repeat-containing protein 8E	0.29	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				795
O75019 UniProt NPD GO	LIRA1_HUMAN	Leukocyte immunoglobulin-like receptor subfamily A member 1 precursor (Leukocyte immunoglobulin-like ...	0.29	-	exc	0	Membrane; single-pass type I membrane protein		604810		489
Q01584 UniProt NPD GO	LIPO_BUFMA	Lipocalin precursor	0.29	-	exc	0	Secreted protein. Found in cerebrospinal fluid				183
Q9JID6 UniProt NPD GO	ACSL1_CAVPO	Long-chain-fatty-acid--CoA ligase 1 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 1) (LACS 1) (Palmit ...	0.29	-	cyt	1 *	Microsome; microsomal membrane; peripheral membrane protein. Mitochondrion; mitochondrial outer memb ...				698
P33124 UniProt NPD GO	ACSL6_RAT	Long-chain-fatty-acid--CoA ligase 6 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 6) (LACS 6) (Long-c ...	0.29	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				697
P20611 UniProt NPD GO	PPAL_RAT	Lysosomal acid phosphatase precursor (EC 3.1.3.2) (LAP)	0.29	-	end	2 *	Lysosome	synaptosome [IDA]			423
P70699 UniProt NPD GO	LYAG_MOUSE	Lysosomal alpha-glucosidase precursor (EC 3.2.1.20) (Acid maltase)	0.29	-	mit	1 *	Lysosome	lysosome [TAS]			953
P14562 UniProt NPD GO	LAMP1_RAT	Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) (120 kDa lysosomal membrane glycoprot ...	0.29	-	exc	1	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...				407
Q99MN1 UniProt NPD GO	SYK_MOUSE	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.29	-	cyt	0	Cytoplasm				595
Q7Z304 UniProt NPD GO	MAMC2_HUMAN	MAM domain-containing protein 2 precursor	0.29	-	exc	0	Secreted protein (Potential)				686
Q9NVU1 UniProt NPD GO	MC3AP_HUMAN	MCM3-associated gene antisense protein	0.29	-	nuc	0					122
P24452 UniProt NPD GO	CAPG_MOUSE	Macrophage capping protein (Myc basic motif homolog 1) (Actin-capping protein GCAP39)	0.29	-	cyt	0	Nucleus. Cytoplasm. Secreted protein. Nuclear GCAP39 redistributes throughout the cytoplasm during m ...				352
Q9GSU7 UniProt NPD GO	HSP71_DROSI	Major heat shock 70 kDa protein Ab (Heat shock protein Hsp70Ab) (HSP70-87C1)	0.29	-	cyt	0					644
Q01493 UniProt NPD GO	GP22_LITCA	Major microfilarial sheath protein precursor	0.29	-	nuc	0					148
Q9QXP6 UniProt NPD GO	MKRN1_MOUSE	Makorin-1	0.29	-	nuc	0					481
P08216 UniProt NPD GO	MASY_CUCSA	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.29	-	pox	0	Glyoxysome				568
Q9Y8C7 UniProt NPD GO	MAT1_COCEL	Mating-type protein MAT-1	0.29	-	cyt	0	Nucleus (Potential)				378
Q33119 UniProt NPD GO	MATK_SAXME	Maturase K (Intron maturase) (Fragment)	0.29	-	nuc	0	Plastid; chloroplast				353
P05512 UniProt NPD GO	RF3_SACBA	Maturase-like RF3 protein	0.29	-	nuc	0					476
Q58T68 UniProt NPD GO	M3H31_BOMMX	Maximins 3/H3 type 1 precursor [Contains: Maximin-3; Maximin-H3]	0.29	-	end	0	Secreted protein				145
P16523 UniProt NPD GO	MER1_YEAST	Meiotic recombination 1 protein	0.29	-	cyt	0		nucleus [IDA]			270
P40385 UniProt NPD GO	REC6_SCHPO	Meiotic recombination protein rec6	0.29	-	nuc	0					182
P15529 UniProt NPD GO	MCP_HUMAN	Membrane cofactor protein precursor (Trophoblast leukocyte common antigen) (TLX) (CD46 antigen)	0.29	-	end	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein. Inner acrosomal membrane of ...	integral to plasma membrane [TAS] plasma membrane [NAS]	120920	1HR4	392
P35624 UniProt NPD GO	TIMP1_PIG	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.29	-	nuc	0	Secreted protein				207
P15787 UniProt NPD GO	MT2_COLLI	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.29	-	nuc	0					63
Q7TSB7 UniProt NPD GO	KISS1_RAT	Metastasis-suppressor KiSS-1 precursor (Kisspeptin-1) [Contains: Metastin; Kisspeptin-10 (Metastin45 ...	0.29	-	exc	0	Secreted protein				130
Q13505 UniProt NPD GO	MTX1_HUMAN	Metaxin-1	0.29	-	nuc	1	Mitochondrion; mitochondrial outer membrane (By similarity)	integral to membrane [TAS]	600605		317
O74634 UniProt NPD GO	SYMM_CANAL	Methionyl-tRNA synthetase, mitochondrial (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.29	-	cyt	0	Mitochondrion; mitochondrial matrix				577
P20774 UniProt NPD GO	MIME_HUMAN	Mimecan precursor (Osteoglycin) (Osteoinductive factor) (OIF)	0.29	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		602383		298
O96870 UniProt NPD GO	ALL5_BLOTA	Mite allergen Blo t 5	0.29	-	vac	0					134
P23369 UniProt NPD GO	RM25_YEAST	Mitochondrial 60S ribosomal protein L25 (YmL25)	0.29	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			156
Q757S0 UniProt NPD GO	TIM9_ASHGO	Mitochondrial import inner membrane translocase subunit TIM9	0.29	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q6DEM5 UniProt NPD GO	TIM8A_BRARE	Mitochondrial import inner membrane translocase subunit Tim8 A	0.29	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
P35848 UniProt NPD GO	TOM20_NEUCR	Mitochondrial import receptor subunit tom-20 (Mitochondrial 20 kDa outer membrane protein) (Transloc ...	0.29	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				181
O94737 UniProt NPD GO	MAPK1_PNECA	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (MAP kinase Mkp1)	0.29	-	cyt	0					370
Q9I958 UniProt NPD GO	MK14B_CYPCA	Mitogen-activated protein kinase 14b (EC 2.7.11.24) (Mitogen-activated protein kinase p38b) (MAP kin ...	0.29	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			361
Q91Y86 UniProt NPD GO	MK08_MOUSE	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (Stress-activated protein kinase JNK1) (c-Jun N-te ...	0.29	-	cyt	0					384
P49185 UniProt NPD GO	MK08_RAT	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (Stress-activated protein kinase JNK1) (c-Jun N-te ...	0.29	-	cyt	0					411
Q90327 UniProt NPD GO	MK08A_CYPCA	Mitogen-activated protein kinase 8A (EC 2.7.11.24) (Stress-activated protein kinase JNKa) (c-Jun N-t ...	0.29	-	cyt	0					427
Q6FIU2 UniProt NPD GO	HOG1_CANGA	Mitogen-activated protein kinase HOG1 (EC 2.7.11.24) (MAP kinase HOG1)	0.29	-	cyt	0					447
Q40517 UniProt NPD GO	NTF3_TOBAC	Mitogen-activated protein kinase homolog NTF3 (EC 2.7.11.24) (P43)	0.29	-	cyt	0					372
Q17446 UniProt NPD GO	PMK1_CAEEL	Mitogen-activated protein kinase pmk-1 (EC 2.7.11.24) (p38 MAP kinase 1) (Stress-activated protein k ...	0.29	-	cyt	0					377
Q9WVA3 UniProt NPD GO	BUB3_MOUSE	Mitotic checkpoint protein BUB3 (WD repeat type I transmembrane protein A72.5)	0.29	-	cyt	0	Nucleus (By similarity)				326
O62820 UniProt NPD GO	MOTI_BOVIN	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.29	-	exc	0	Secreted protein				115

You are viewing entries 41451 to 41500 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.