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
P40513 UniProt NPD GO	MAM33_YEAST	Mitochondrial acidic protein MAM33, mitochondrial precursor	0.18	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			266
Q6EIX2 UniProt NPD GO	TIM16_RAT	Mitochondrial import inner membrane translocase subunit TIM16 (Mitochondria-associated granulocyte m ...	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				124
Q9W2D6 UniProt NPD GO	TIM10_DROME	Mitochondrial import inner membrane translocase subunit Tim10	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	mitochondrial intermembrane space protein t... [ISS]			92
Q6P321 UniProt NPD GO	TIM10_XENTR	Mitochondrial import inner membrane translocase subunit Tim10	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
Q9XGY4 UniProt NPD GO	TIM8_ARATH	Mitochondrial import inner membrane translocase subunit Tim8	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				77
Q3SZ93 UniProt NPD GO	TIM8B_BOVIN	Mitochondrial import inner membrane translocase subunit Tim8 B	0.18	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				83
Q9VYD7 UniProt NPD GO	TIM9_DROME	Mitochondrial import inner membrane translocase subunit Tim9	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q5AZH4 UniProt NPD GO	TIM13_EMENI	Mitochondrial import inner membrane translocase subunit tim13	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				108
Q10481 UniProt NPD GO	TIM13_SCHPO	Mitochondrial import inner membrane translocase subunit tim13	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q9USM7 UniProt NPD GO	TIM23_SCHPO	Mitochondrial import inner membrane translocase subunit tim23	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...				210
P34227 UniProt NPD GO	PRX1_YEAST	Mitochondrial peroxiredoxin PRX1 (EC 1.11.1.15) (Thioredoxin reductase) (1-Cys PRX) (Mitochondrial t ...	0.18	-	mit	0	Mitochondrion	mitochondrion [IDA]			261
Q8M355 UniProt NPD GO	RMAR_SACCA	Mitochondrial ribosomal protein VAR1	0.18	-	nuc	0	Mitochondrion				326
Q8QHK8 UniProt NPD GO	MK08_XENLA	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (Stress-activated protein kinase JNK1)	0.18	-	cyt	0					426
Q28680 UniProt NPD GO	CD14_RABIT	Monocyte differentiation antigen CD14 precursor (Myeloid cell-specific leucine-rich glycoprotein)	0.18	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor				372
Q9UJG1 UniProt NPD GO	MSPD1_HUMAN	Motile sperm domain-containing protein 1	0.18	-	end	2	Membrane; multi-pass membrane protein (Potential)				213
Q5RCC7 UniProt NPD GO	MSPD1_PONPY	Motile sperm domain-containing protein 1	0.18	-	end	2	Membrane; multi-pass membrane protein (Potential)				213
P06795 UniProt NPD GO	MDR1_MOUSE	Multidrug resistance protein 1 (EC 3.6.3.44) (P-glycoprotein 1) (CD243 antigen)	0.18	-	end	10 *	Membrane; multi-pass membrane protein	intercellular canaliculus [IDA]			1276
Q5F364 UniProt NPD GO	MRP1_CHICK	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.18	-	end	14 *	Membrane; multi-pass membrane protein (By similarity)				1525
Q53IP3 UniProt NPD GO	MBF1_GIBFU	Multiprotein-bridging factor 1	0.18	-	nuc	0					152
P41986 UniProt NPD GO	ACM4_BOVIN	Muscarinic acetylcholine receptor M4 (Fragment)	0.18	-	nuc	0	Membrane; multi-pass membrane protein				126
Q24621 UniProt NPD GO	MLC1_DROPS	Myosin light chain alkali	0.18	+	cyt	0		muscle myosin [ISS]			155
Q24756 UniProt NPD GO	MLC1_DROVI	Myosin light chain alkali	0.18	+	cyt	0		muscle myosin [ISS]			155
P81271 UniProt NPD GO	MYH11_PIG	Myosin-11 (Myosin heavy chain, smooth muscle isoform) (SMMHC) (Fragments)	0.18	-	cyt	0	Thick filaments of the myofibrils				65
Q5EA01 UniProt NPD GO	B3GN6_BOVIN	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase (EC 2.4.1.149) (Poly-N-acetyllactosam ...	0.18	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				415
Q9M274 UniProt NPD GO	NAC66_ARATH	NAC domain-containing protein 66 (ANAC066) (NAC SECONDARY WALL THICKENING PROMOTING FACTOR 2)	0.18	-	nuc	0	Nucleus (Probable)				334
Q85CP2 UniProt NPD GO	NU2C_ANTFO	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.18	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				500
Q7YJT3 UniProt NPD GO	NU4C_CALFE	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.18	-	end	14 *	Plastid; chloroplast				502
Q32007 UniProt NPD GO	NU5C_CICIN	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.18	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				741
P15958 UniProt NPD GO	NU5C_VICFA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.18	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				746
P92248 UniProt NPD GO	NU5C_BRAPI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.18	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				214
Q85FH1 UniProt NPD GO	NUIC_ADICA	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.18	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
O09111 UniProt NPD GO	NDUBB_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial precursor (EC 1.6.5.3) ( ...	0.18	-	nuc	1	Mitochondrion; mitochondrial inner membrane (Potential)	mitochondrion [IDA]			151
P00387 UniProt NPD GO	NCB5R_HUMAN	NADH-cytochrome b5 reductase (EC 1.6.2.2) (B5R) (Diaphorase-1) (Cytochrome b5 reductase 3) [Contains ...	0.18	-	mit	0	Isoform 1: Endoplasmic reticulum; endoplasmic reticulum membrane; lipid-anchor; cytoplasmic side. Mi ...	cytoplasm [TAS] hemoglobin complex [TAS] membrane [TAS]	250800	1UMK	300
Q9TAJ7 UniProt NPD GO	NUCM_CAFRO	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.18	-	cyt	0	Mitochondrion				398
P15689 UniProt NPD GO	NUCM_PARTE	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.18	-	cyt	0	Mitochondrion				400
Q70Y28 UniProt NPD GO	NU1M_CYCDI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.18	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q9T9X9 UniProt NPD GO	NU1M_PONPY	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O63767 UniProt NPD GO	NU2M_ANAAC	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
O63794 UniProt NPD GO	NU2M_ANAAM	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
O63797 UniProt NPD GO	NU2M_ANAFA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
O63798 UniProt NPD GO	NU2M_ANAPE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
Q2I3H3 UniProt NPD GO	NU2M_ELEMA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q8LX31 UniProt NPD GO	NU2M_LEMCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q9ZXY3 UniProt NPD GO	NU2M_PAPHA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	exc	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q85PQ0 UniProt NPD GO	NU2M_PARHE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q95910 UniProt NPD GO	NU2M_POLOR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
Q2TQ17 UniProt NPD GO	NU2M_SYLGA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q85PQ1 UniProt NPD GO	NU2M_VIVTA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.18	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P38601 UniProt NPD GO	NU4M_HALGR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.18	-	end	12 *					459
P03920 UniProt NPD GO	NU5M_BOVIN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.18	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606

You are viewing entries 53301 to 53350 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.