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
Q13405 UniProt NPD GO	RM49_HUMAN	Mitochondrial 39S ribosomal protein L49 (L49mt) (MRP-L49) (Protein NOF1) (Neighbor of FAU) (NOF)	0.21	-	mit	0	Mitochondrion		606866		166
P42834 UniProt NPD GO	MDJ2_YEAST	Mitochondrial DnaJ homolog 2	0.21	-	nuc	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] presequence translocase-associated import m... [IPI]			146
Q5ZM83 UniProt NPD GO	MIRO2_CHICK	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.21	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				618
P53299 UniProt NPD GO	TIM13_YEAST	Mitochondrial import inner membrane translocase subunit TIM13	0.21	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial intermembrane space protein t... [IDA]			105
Q6C331 UniProt NPD GO	TIM16_YARLI	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				147
P57744 UniProt NPD GO	TIM8_YEAST	Mitochondrial import inner membrane translocase subunit TIM8	0.21	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side. Import ...	mitochondrial intermembrane space protein t... [IDA]			87
O74700 UniProt NPD GO	TIM9_YEAST	Mitochondrial import inner membrane translocase subunit TIM9	0.21	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial intermembrane space protein t... [IDA]			87
Q9UTE9 UniProt NPD GO	TIM10_SCHPO	Mitochondrial import inner membrane translocase subunit tim10	0.21	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
P48849 UniProt NPD GO	RMAR_PICCA	Mitochondrial ribosomal protein VAR1	0.21	-	nuc	0	Mitochondrion				386
Q9Y8B5 UniProt NPD GO	MPPB_LENED	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP)	0.21	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				466
P28482 UniProt NPD GO	MK01_HUMAN	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (Extracellular signal-regulated kinase 2) (ERK-2) ...	0.21	-	cyt	0			176948	1WZY	359
P49187 UniProt NPD GO	MK10_RAT	Mitogen-activated protein kinase 10 (EC 2.7.11.24) (Stress-activated protein kinase JNK3) (c-Jun N-t ...	0.21	-	cyt	0					464
P40417 UniProt NPD GO	ERKA_DROME	Mitogen-activated protein kinase ERK-A (EC 2.7.11.24) (Extracellular-regulated kinase A) (Protein ro ...	0.21	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			376
P39047 UniProt NPD GO	MYTR_MITCE	Mitrocomin precursor	0.21	-	cyt	0					198
Q7YWV6 UniProt NPD GO	MPV17_CAEEL	Mpv17-like protein	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				181
Q9LZJ5 UniProt NPD GO	MRP10_ARATH	Multidrug resistance-associated protein 10 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPas ...	0.21	-	end	16 *	Membrane; multi-pass membrane protein (Potential)				1539
P20916 UniProt NPD GO	MAG_HUMAN	Myelin-associated glycoprotein precursor (Siglec-4a)	0.21	-	end	1	Membrane; single-pass type I membrane protein		159460		626
Q24799 UniProt NPD GO	MYPH_ECHGR	Myophilin	0.21	-	nuc	0					190
P24331 UniProt NPD GO	MYX1_CRODU	Myotoxin-1 precursor (Crotamine-1)	0.21	-	nuc	0	Secreted protein				65
P29737 UniProt NPD GO	MYR1_SINAL	Myrosinase MB1 (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase) (Fragment)	0.21	-	cyt	0	Vacuole				244
P81613 UniProt NPD GO	MYTB_MYTED	Mytilin-B	0.21	-	mit	0	Secreted protein				34
P43605 UniProt NPD GO	ECO1_YEAST	N-acetyltransferase ECO1 (EC 2.3.1.-) (Establishment of cohesion protein 1) (Chromosome transmission ...	0.21	-	nuc	0	Nucleus. Associated with chromatin	nuclear chromatin [IDA]			281
Q9C932 UniProt NPD GO	NAC19_ARATH	NAC domain-containing protein 19 (ANAC019) (ANAC) (Abscicic-acid-responsive NAC)	0.21	-	cyt	0	Nucleus			1UT7	317
P51095 UniProt NPD GO	NU5C_ADEHI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.21	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				744
P51097 UniProt NPD GO	NU5C_ASTCO	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.21	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				741
Q32091 UniProt NPD GO	NU5C_CARTI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.21	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				743
Q6L3E3 UniProt NPD GO	NU5C_SACHY	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.21	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				738
Q6ENQ0 UniProt NPD GO	NU5C_SACOF	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.21	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				738
P25709 UniProt NPD GO	NUCC_MAIZE	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.21	-	cyt	0	Plastid; chloroplast				393
Q32RK1 UniProt NPD GO	NUIC_ZYGCR	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.21	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				181
P37224 UniProt NPD GO	MAOM_AMAHP	NAD-dependent malic enzyme 65 kDa isoform, mitochondrial precursor (EC 1.1.1.39) (NAD-ME)	0.21	-	mit	0	Mitochondrion; mitochondrial matrix				623
O43920 UniProt NPD GO	NIPM_HUMAN	NADH-ubiquinone oxidoreductase 15 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-15 kDa) (CI-15 k ...	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side		603847		105
O79546 UniProt NPD GO	NU1M_DINSE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.21	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				321
P03893 UniProt NPD GO	NU2M_MOUSE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.21	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
O78748 UniProt NPD GO	NU2M_SHEEP	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.21	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TQ19 UniProt NPD GO	NU2M_SYLLU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.21	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2I3G5 UniProt NPD GO	NU4M_ELEMA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.21	-	end	13 *					459
O79556 UniProt NPD GO	NU5M_DINSE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.21	-	end	13 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				590
Q38PR2 UniProt NPD GO	NU5M_MAMPR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.21	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
P28998 UniProt NPD GO	DHE4_CHLSO	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (Fragment)	0.21	-	mit	0	Plastid; chloroplast				523
Q61578 UniProt NPD GO	ADRO_MOUSE	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor (EC 1.18.1.2) (Adrenodoxin reductase) (AR) ...	0.21	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			494
Q6NTW6 UniProt NPD GO	ULA1_XENLA	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (APP-BP1)	0.21	-	nuc	0					533
P27814 UniProt NPD GO	KLRBC_MOUSE	Natural killer cell surface protein P1-40 (NKR-P1 40) (NKR-P1.9)	0.21	-	nuc	1 *	Membrane; single-pass type II membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IDA]			220
P19621 UniProt NPD GO	NEP_PIG	Neprilysin (EC 3.4.24.11) (Neutral endopeptidase) (NEP) (Enkephalinase) (Neutral endopeptidase 24.11 ...	0.21	-	mit	0	Membrane; single-pass type II membrane protein				26
O15394 UniProt NPD GO	NCAM2_HUMAN	Neural cell adhesion molecule 2 precursor (N-CAM 2)	0.21	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] plasma membrane [TAS]	602040		837
O00533 UniProt NPD GO	CHL1_HUMAN	Neural cell adhesion molecule L1-like protein precursor (Close homolog of L1)	0.21	-	end	1	Membrane; single-pass type I membrane protein. Soluble forms produced by cleavage/shedding also exis ...	integral to membrane [TAS]	607416		1208
P35608 UniProt NPD GO	NF1_CHICK	Neurofibromin (Neurofibromatosis-related protein NF-1) (Fragment)	0.21	-	cyt	0					270
P34962 UniProt NPD GO	NEUU_CANFA	Neuromedin U-25 (NmU-25) [Contains: Neuromedin U-8 (NmU-8)]	0.21	-	cyt	0	Secreted protein				25
Q9WVD0 UniProt NPD GO	NPY1R_CAVPO	Neuropeptide Y receptor type 1 (NPY1-R)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				383
O02835 UniProt NPD GO	NPY1R_PIG	Neuropeptide Y receptor type 1 (NPY1-R)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				383

You are viewing entries 49751 to 49800 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.