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
P62507 UniProt NPD GO	RM44_ASHGO	Mitochondrial 60S ribosomal protein L44	0.23	-	mit	0	Mitochondrion (By similarity)				98
P40464 UniProt NPD GO	FLX1_YEAST	Mitochondrial FAD carrier protein FLX1	0.23	+	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			311
Q8IMX7 UniProt NPD GO	MIRO_DROME	Mitochondrial Rho GTPase (EC 3.6.5.-) (Miro) (dMiro)	0.23	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (Probable)				652
Q6DIS1 UniProt NPD GO	MIRO2_XENTR	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.23	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				616
Q4IPZ1 UniProt NPD GO	TIM10_GIBZE	Mitochondrial import inner membrane translocase subunit TIM10	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q07914 UniProt NPD GO	TIM14_YEAST	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	presequence translocase-associated import m... [IPI]			168
Q9Y3D7 UniProt NPD GO	TIM16_HUMAN	Mitochondrial import inner membrane translocase subunit TIM16 (Mitochondria-associated granulocyte m ...	0.23	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				125
Q6BU42 UniProt NPD GO	TIM9_DEBHA	Mitochondrial import inner membrane translocase subunit TIM9	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				78
Q6CM57 UniProt NPD GO	TIM9_KLULA	Mitochondrial import inner membrane translocase subunit TIM9	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q4V7R1 UniProt NPD GO	TIM9_XENLA	Mitochondrial import inner membrane translocase subunit Tim9	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
P35180 UniProt NPD GO	TOM20_YEAST	Mitochondrial import receptor subunit TOM20 (Mitochondrial 20 kDa outer membrane protein) (Transloca ...	0.23	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane translocase co... [TAS]			183
P46760 UniProt NPD GO	RT13_ACACA	Mitochondrial ribosomal protein S13	0.23	-	nuc	0	Mitochondrion				119
P46761 UniProt NPD GO	RT14_ACACA	Mitochondrial ribosomal protein S14	0.23	-	nuc	0	Mitochondrion				99
Q9Y3D9 UniProt NPD GO	RT23_HUMAN	Mitochondrial ribosomal protein S23 (S23mt) (MRP-S23)	0.23	-	cyt	0	Mitochondrion				190
Q8VE22 UniProt NPD GO	RT23_MOUSE	Mitochondrial ribosomal protein S23 (S23mt) (MRP-S23)	0.23	-	cyt	0	Mitochondrion				177
Q39021 UniProt NPD GO	MPK1_ARATH	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (MAP kinase 1) (AtMPK1)	0.23	-	cyt	0					370
Q15759 UniProt NPD GO	MK11_HUMAN	Mitogen-activated protein kinase 11 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 beta) (MAP ...	0.23	-	cyt	0			602898		372
Q16539 UniProt NPD GO	MK14_HUMAN	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 alpha) (MAP ...	0.23	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]	600289	2BAQ	359
O62618 UniProt NPD GO	MK14A_DROME	Mitogen-activated protein kinase 14A (EC 2.7.11.24) (MAP kinase p38a) (p38 MAPK) (Dp38) (D-p38a)	0.23	-	cyt	0	Nucleus				366
O35910 UniProt NPD GO	MOT4_RAT	Monocarboxylate transporter 4 (MCT 4) (MCT 3)	0.23	-	end	12 *	Cell membrane; multi-pass membrane protein				471
P10810 UniProt NPD GO	CD14_MOUSE	Monocyte differentiation antigen CD14 precursor (Myeloid cell-specific leucine-rich glycoprotein)	0.23	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor			1WWL	366
P0C195 UniProt NPD GO	CXM3A_CONKI	Mu-conotoxin KIIIA	0.23	-		0	Secreted protein (By similarity)				18
Q60HE8 UniProt NPD GO	MCLN1_MACFA	Mucolipin-1 (Mucolipidin)	0.23	-	end	5	Cell membrane; multi-pass membrane protein (By similarity). Endosome; late endosome; late endosomal ...				580
Q9M1Q9 UniProt NPD GO	MDR17_ARATH	Multidrug resistance protein 17 (P-glycoprotein 21)	0.23	-	end	9	Membrane; multi-pass membrane protein (Potential)				1292
P23174 UniProt NPD GO	MDR3_CRIGR	Multidrug resistance protein 3 (EC 3.6.3.44) (P-glycoprotein 3)	0.23	-	end	11	Membrane; multi-pass membrane protein				1281
Q6UR05 UniProt NPD GO	MRP1_CANFA	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.23	-	end	14 *	Membrane; multi-pass membrane protein (By similarity)				1531
Q6AYT8 UniProt NPD GO	MPZL1_RAT	Myelin protein zero-like protein 1 precursor	0.23	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				270
P70402 UniProt NPD GO	MYBPH_MOUSE	Myosin-binding protein H (MyBP-H) (H-protein)	0.23	-	nuc	0					483
P24332 UniProt NPD GO	MYX2_CRODU	Myotoxin-2 precursor (Crotamine-2) (Fragment)	0.23	-	nuc	0	Secreted protein				64
Q64323 UniProt NPD GO	PIGA_MOUSE	N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein (GlcNAc-PI synthesis protein) (Phosph ...	0.23	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [ISS] glycosylphosphatidylinositol-N-acetylglucos... [ISS]			485
P51099 UniProt NPD GO	NU5C_ATRJA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.23	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				749
Q9TLA3 UniProt NPD GO	NU5C_LIGVU	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.23	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				738
P46620 UniProt NPD GO	NU5C_MAIZE	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.23	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				738
Q500Y9 UniProt NPD GO	NADHK_ARATH	NADH kinase (EC 2.7.1.86) (AtNADK-3)	0.23	-	nuc	0	Cytoplasm				317
Q43844 UniProt NPD GO	NUKM_SOLTU	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.23	-	mit	0					213
P24971 UniProt NPD GO	NU2M_COTJA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.23	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
P41305 UniProt NPD GO	NU2M_DIDMA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.23	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O79547 UniProt NPD GO	NU2M_DINSE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.23	-	nuc	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				343
O99817 UniProt NPD GO	NU2M_RHISA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.23	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				313
O63908 UniProt NPD GO	NU5M_MYOGL	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.23	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
Q953I4 UniProt NPD GO	NU5M_SORFM	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.23	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
Q09765 UniProt NPD GO	UBA3_SCHPO	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme E1 3)	0.23	-	nuc	0					444
Q6DGL2 UniProt NPD GO	KBRS2_BRARE	NF-kappa-B inhibitor-interacting Ras-like protein 2 (I-kappa-B-interacting Ras-like protein 2) (Kapp ...	0.23	-	cyt	0	Cytoplasm (By similarity)				192
O08557 UniProt NPD GO	DDAH1_RAT	NG,NG-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) (Dimethylargininase-1) (Dimethylargini ...	0.23	-	nuc	0					284
P41090 UniProt NPD GO	FL3H_VITVI	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT)	0.23	-	cyt	0					364
Q9M612 UniProt NPD GO	NACA_PINTA	Nascent polypeptide-associated complex subunit alpha-like protein (NAC-alpha-like protein) (Alpha-NA ...	0.23	-	nuc	0					205
Q02642 UniProt NPD GO	EGD1_YEAST	Nascent polypeptide-associated complex subunit beta EGD2 (NAC-beta) (Beta-NAC) (BTF3 homolog EGD1) ( ...	0.23	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic, may also transiently localize to the nucleus	cytosolic ribosome (sensu Eukaryota) [TAS] nascent polypeptide-associated complex [IDA]			157
P27812 UniProt NPD GO	KLRBB_MOUSE	Natural killer cell surface protein P1-34 (NKR-P1 34)	0.23	-	nuc	1 *	Membrane; single-pass type II membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IDA]			223
Q9MZK9 UniProt NPD GO	KLRD1_MACMU	Natural killer cells antigen CD94 (NK cell receptor) (Killer cell lectin-like receptor subfamily D m ...	0.23	-	nuc	1 *	Membrane; single-pass type II membrane protein				179
Q6C7U8 UniProt NPD GO	PHO85_YARLI	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85)	0.23	-	cyt	0					294

You are viewing entries 47601 to 47650 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.