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
P34949 UniProt NPD GO	MANA_HUMAN	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.17	-	cyt	0	Cytoplasm (Probable)		602579		422
O46683 UniProt NPD GO	MCPT3_SHEEP	Mast cell protease 3 precursor (EC 3.4.21.-) (SMCP-3)	0.17	-	exc	0	Secretory granules				251
P19392 UniProt NPD GO	MATA_NEUCR	Mating-type protein A-1 (Mt A-1)	0.17	-	nuc	0	Nucleus (Potential)				293
Q9P7N0 UniProt NPD GO	MEU32_SCHPO	Meiotic expression up-regulated protein 32	0.17	-	cyt	0					392
Q8MJ88 UniProt NPD GO	MCHR2_MACMU	Melanin-concentrating hormone receptor 2 (MCH receptor 2) (MCHR-2) (MCH-R2) (MCH2R) (MCH-2R) (MCH2) ...	0.17	-	end	7 *	Membrane; multi-pass membrane protein				340
Q8SQ54 UniProt NPD GO	MCHR2_MACFA	Melanin-concentrating hormone receptor 2 (MCH receptor 2) (MCHR-2) (MCH-R2) (MCH2R) (MCH-2R) (MCH2) ...	0.17	-	end	7 *	Membrane; multi-pass membrane protein				340
P51051 UniProt NPD GO	MTR1B_XENLA	Melatonin receptor type 1B X1.7 (MEL-1B-R) (Fragment)	0.17	-	end	3 *	Membrane; multi-pass membrane protein				152
P68407 UniProt NPD GO	MEL_APICC	Melittin precursor	0.17	-	exc	2 *	Secreted protein (By similarity)				70
Q8LW54 UniProt NPD GO	MEL_APICE	Melittin precursor	0.17	-	mit	0	Secreted protein (By similarity)				77
O00264 UniProt NPD GO	PGRC1_HUMAN	Membrane-associated progesterone receptor component 1 (mPR)	0.17	-	nuc	1 *	Microsome; microsomal membrane; single-pass membrane protein (By similarity)	cell surface [IEP] integral to plasma membrane [TAS]	300435		194
P58280 UniProt NPD GO	MT1_BOVIN	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.17	-	nuc	0					61
P02805 UniProt NPD GO	MT1_SCYSE	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.17	-	nuc	0					58
Q9D125 UniProt NPD GO	RT25_MOUSE	Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25)	0.17	-	cyt	0	Mitochondrion (By similarity)	mitochondrion [IDA]			171
Q5R8X0 UniProt NPD GO	RM49_PONPY	Mitochondrial 39S ribosomal protein L49 (L49mt) (MRP-L49)	0.17	-	mit	0	Mitochondrion				166
P35719 UniProt NPD GO	RT08_YEAST	Mitochondrial 40S ribosomal protein MRP8 (Mitochondrial ribosomal protein 8)	0.17	-	cyt	0	Mitochondrion				219
Q95747 UniProt NPD GO	RM16_ARATH	Mitochondrial 60S ribosomal protein L16	0.17	-	mit	0	Mitochondrion				179
Q5E9M9 UniProt NPD GO	MIRO2_BOVIN	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.17	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				618
P32839 UniProt NPD GO	BCS1_YEAST	Mitochondrial chaperone BCS1	0.17	-	cyt	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	mitochondrial inner membrane [IDA]			456
Q6FPC0 UniProt NPD GO	TIM54_CANGA	Mitochondrial import inner membrane translocase subunit TIM54	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				452
Q6FK81 UniProt NPD GO	TIM8_CANGA	Mitochondrial import inner membrane translocase subunit TIM8	0.17	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q9SP35 UniProt NPD GO	TIM17_ARATH	Mitochondrial import inner membrane translocase subunit Tim17	0.17	-	gol	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				243
Q9Y1A3 UniProt NPD GO	TIM8_DROME	Mitochondrial import inner membrane translocase subunit Tim8	0.17	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				88
Q9WV98 UniProt NPD GO	TIM9_MOUSE	Mitochondrial import inner membrane translocase subunit Tim9	0.17	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
Q7S6S4 UniProt NPD GO	TIM16_NEUCR	Mitochondrial import inner membrane translocase subunit tim-16 (Presequence translocated-associated ...	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				141
Q4WI88 UniProt NPD GO	TIM14_ASPFU	Mitochondrial import inner membrane translocase subunit tim14 (Presequence translocated-associated m ...	0.17	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				105
Q5B4H1 UniProt NPD GO	TIM14_EMENI	Mitochondrial import inner membrane translocase subunit tim14 (Presequence translocated-associated m ...	0.17	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				105
Q9FNC9 UniProt NPD GO	TO222_ARATH	Mitochondrial import receptor subunit TOM22 homolog 2 (Translocase of outer membrane 22 kDa subunit ...	0.17	-	mit	1	Mitochondrion; mitochondrial outer membrane; single-pass type II membrane protein				98
Q92377 UniProt NPD GO	MDM12_SCHPO	Mitochondrial inheritance component mdm12	0.17	-	cyt	0	Mitochondrion; mitochondrial outer membrane				273
Q8N4Q1 UniProt NPD GO	MIA40_HUMAN	Mitochondrial intermembrane space import and assembly protein 40 (Coiled-coil-helix-coiled-coil-heli ...	0.17	-	nuc	0	Mitochondrion; mitochondrial intermembrane space				142
P47906 UniProt NPD GO	RMAR_WILMR	Mitochondrial ribosomal protein VAR1	0.17	-	nuc	0	Mitochondrion				380
O42376 UniProt NPD GO	MK12_BRARE	Mitogen-activated protein kinase 12 (EC 2.7.11.24) (Stress-activated protein kinase 3)	0.17	-	cyt	0	Cytoplasm (By similarity)				363
Q6Z437 UniProt NPD GO	MPK3_ORYSA	Mitogen-activated protein kinase 3 (EC 2.7.11.24) (MAP kinase 3) (OsMAP3) (MAP kinase 2) (OsMAPK2)	0.17	-	cyt	0					370
O42860 UniProt NPD GO	BUB3_SCHPO	Mitotic checkpoint protein bub3	0.17	-	nuc	0	Nucleus. Associates with kinetochores and centromeres during the early stages of mitosis				320
Q40977 UniProt NPD GO	MDAR_PEA	Monodehydroascorbate reductase (EC 1.6.5.4) (MDAR) (Ascorbate free radical reductase) (AFR reductase ...	0.17	-	cyt	0	Cytoplasm (Probable)				433
Q9XSE2 UniProt NPD GO	MOTI_FELCA	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.17	-	exc	1 *	Secreted protein				116
Q91510 UniProt NPD GO	VSP4_TRIMU	Mucrofibrase-4 precursor (EC 3.4.21.-)	0.17	-	exc	0	Secreted protein				257
Q8CG09 UniProt NPD GO	MRP1_RAT	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.17	-	end	16 *	Membrane; multi-pass membrane protein (By similarity)				1532
Q752P7 UniProt NPD GO	MBF1_ASHGO	Multiprotein-bridging factor 1	0.17	-	nuc	0					152
P02691 UniProt NPD GO	MYP2_RABIT	Myelin P2 protein	0.17	-	cyt	0					131
Q8IDR3 UniProt NPD GO	MYOA_PLAF7	Myosin A (PfM-A)	0.17	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Tightly associated wit ...				818
Q9UAR6 UniProt NPD GO	MYOA_PLAFB	Myosin A (PfM-A)	0.17	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Tightly associated wit ...				818
P29092 UniProt NPD GO	MYR3_SINAL	Myrosinase MB3 precursor (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase)	0.17	-	exc	0	Vacuole				544
P11024 UniProt NPD GO	NNTM_BOVIN	NAD(P) transhydrogenase, mitochondrial precursor (EC 1.6.1.2) (Pyridine nucleotide transhydrogenase) ...	0.17	-	end	11	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (Potential)			1D4O	1086
Q85FH5 UniProt NPD GO	NU4C_ADICA	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.17	-	end	14 *	Plastid; chloroplast				497
Q85BG0 UniProt NPD GO	NU4C_ANTFO	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.17	-	end	15 *	Plastid; chloroplast				501
Q8WHX8 UniProt NPD GO	NU4C_PSINU	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.17	-	end	14 *	Plastid; chloroplast				498
Q95H46 UniProt NPD GO	NU5C_WHEAT	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.17	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				739
Q9MVK2 UniProt NPD GO	NU5C_PACAQ	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.17	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				709
O43678 UniProt NPD GO	NDUA2_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side		602137	1S3A	98
Q9DCJ5 UniProt NPD GO	NDUA8_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.17	-	cyt	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			171

You are viewing entries 54551 to 54600 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.