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
O88441 UniProt NPD GO	MTX2_MOUSE	Metaxin-2	0.20	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrion [IDA]			263
Q5I0C5 UniProt NPD GO	FMT_RAT	Methionyl-tRNA formyltransferase, mitochondrial precursor (EC 2.1.2.9) (MtFMT)	0.20	-	mit	0	Mitochondrion (By similarity)				385
Q96RQ3 UniProt NPD GO	MCCA_HUMAN	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4) (3-methylcrotony ...	0.20	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	609010		725
Q9CZD0 UniProt NPD GO	MMAC_MOUSE	Methylmalonic aciduria and homocystinuria type C homolog	0.20	-	cyt	0					279
Q5RDV8 UniProt NPD GO	METL6_PONPY	Methyltransferase-like protein 6 (EC 2.1.1.-)	0.20	-	mit	0					282
Q6BPD6 UniProt NPD GO	SPC3_DEBHA	Microsomal signal peptidase subunit 3 (EC 3.4.-.-)	0.20	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				190
Q9JKF7 UniProt NPD GO	RM39_MOUSE	Mitochondrial 39S ribosomal protein L39 (L39mt) (MRP-L39)	0.20	-	mit	0	Mitochondrion (By similarity)				336
P26860 UniProt NPD GO	RM05_MARPO	Mitochondrial 60S ribosomal protein L5	0.20	-	nuc	0	Mitochondrion				188
Q7TSA0 UniProt NPD GO	MIRO2_RAT	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.20	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				622
Q6CEU0 UniProt NPD GO	TIM14_YARLI	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.20	-	cyt	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				148
O62250 UniProt NPD GO	TIM16_CAEEL	Mitochondrial import inner membrane translocase subunit TIM16	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				136
Q9CQV1 UniProt NPD GO	TIM16_MOUSE	Mitochondrial import inner membrane translocase subunit TIM16 (Mitochondria-associated granulocyte m ...	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA] mitochondrial inner membrane [IDA]			125
Q6NTU3 UniProt NPD GO	TI16A_XENLA	Mitochondrial import inner membrane translocase subunit TIM16-A	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				125
Q17754 UniProt NPD GO	TIM9_CAEEL	Mitochondrial import inner membrane translocase subunit Tim9	0.20	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
Q9WV97 UniProt NPD GO	TIM9_RAT	Mitochondrial import inner membrane translocase subunit Tim9	0.20	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
Q7SBR3 UniProt NPD GO	TIM13_NEUCR	Mitochondrial import inner membrane translocase subunit tim-13	0.20	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				86
P02381 UniProt NPD GO	RMAR_YEAST	Mitochondrial ribosomal protein VAR1	0.20	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			404
P46196 UniProt NPD GO	MK01_BOVIN	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (Extracellular signal-regulated kinase 2) (ERK-2) ...	0.20	-	cyt	0					359
O02812 UniProt NPD GO	MK14_CANFA	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 alpha) (MAP ...	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			359
P70618 UniProt NPD GO	MK14_RAT	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 alpha) (MAP ...	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] cytosol [IDA] nucleus [ISS]			359
Q5XGI5 UniProt NPD GO	MORG1_XENTR	Mitogen-activated protein kinase organizer 1 (MAPK organizer 1)	0.20	-	nuc	0	Cytoplasm (By similarity)				314
P25289 UniProt NPD GO	MPI2_LYMST	Molluscan insulin-related peptide 2 precursor (MIP II) [Contains: Molluscan insulin-related peptide ...	0.20	-	mit	1 *	Secretory granules				137
O61389 UniProt NPD GO	MIH_CANMG	Molt-inhibiting hormone precursor (MIH)	0.20	-	mit	1 *	Secreted protein				113
P36021 UniProt NPD GO	MOT8_HUMAN	Monocarboxylate transporter 8 (MCT 8) (X-linked PEST-containing transporter) (MCT 7)	0.20	-	end	11	Cell membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] membrane fraction [TAS]	300523		613
P32642 UniProt NPD GO	GLRX4_YEAST	Monothiol glutaredoxin-4	0.20	-	cyt	0		intracellular [TAS]			244
Q9HBB8 UniProt NPD GO	MUCDL_HUMAN	Mucin and cadherin-like protein precursor (Mu-protocadherin)	0.20	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS] membrane [NAS]	606839		845
P49000 UniProt NPD GO	MIS_RAT	Muellerian-inhibiting factor precursor (MIS) (Anti-Muellerian hormone) (AMH) (Muellerian-inhibiting ...	0.20	-	vac	0	Secreted protein (By similarity)	extracellular space [IDA]			553
Q9LHD1 UniProt NPD GO	MDR13_ARATH	Multidrug resistance protein 13 (P-glycoprotein 15)	0.20	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1240
Q6BXQ8 UniProt NPD GO	MBF1_DEBHA	Multiprotein-bridging factor 1	0.20	-	nuc	0					150
P79280 UniProt NPD GO	MYLK_PIG	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Fragment)	0.20	-	nuc	0					139
P24333 UniProt NPD GO	MYX3_CRODU	Myotoxin-3 precursor (Crotamine-3)	0.20	-	nuc	0	Secreted protein				65
Q23270 UniProt NPD GO	TRM1_CAEEL	N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2)) methylt ...	0.20	-	cyt	0					526
Q86SF2 UniProt NPD GO	GALT7_HUMAN	N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 7) (UD ...	0.20	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		605005		657
Q32551 UniProt NPD GO	NU5C_MUTAC	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.20	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				744
Q9MVL6 UniProt NPD GO	NU5C_MALAR	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.20	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				707
Q32880 UniProt NPD GO	NU5C_POAPR	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.20	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				702
P12133 UniProt NPD GO	NUCC_TOBAC	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.20	-	cyt	0	Plastid; chloroplast				393
Q9MTH8 UniProt NPD GO	NUIC_OENHO	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.20	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				165
Q6YXP9 UniProt NPD GO	NUIC_PHYPA	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.20	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				181
O97725 UniProt NPD GO	NDUAC_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.20	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				145
Q9UI09 UniProt NPD GO	NDUAC_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.20	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				145
Q9P0J0 UniProt NPD GO	NDUAD_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.20	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein; matrix side. Nucleus. May ...	cytoplasm [IDA] mitochondrial electron transport chain [IDA] mitochondrion [IDA] nucleoplasm [IDA]	609435		143
Q9ERS2 UniProt NPD GO	NDUAD_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.20	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; matrix side (Probable). May be translocated into the nu ...	cytoplasm [ISS] mitochondrial electron transport chain [ISS] mitochondrion [IDA] nucleoplasm [ISS] nucleus [IDA]			143
Q4FZG9 UniProt NPD GO	NUA4L_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4-like 2	0.20	-	nuc	1 *					87
Q02366 UniProt NPD GO	NDUA6_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				127
P56556 UniProt NPD GO	NDUA6_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.20	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side		602138		127
O21272 UniProt NPD GO	NUKM_RECAM	NADH-ubiquinone oxidoreductase 20 kDa subunit (EC 1.6.5.3) (NADH dehydrogenase subunit 10)	0.20	-	cyt	0					182
P42027 UniProt NPD GO	NUKM_BRAOL	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.20	-	mit	0					215
P92690 UniProt NPD GO	NU1M_PONPA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.20	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P24972 UniProt NPD GO	NU2M_CYPCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.20	-	nuc	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348

You are viewing entries 50851 to 50900 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.