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
P28184 UniProt NPD GO	MT3_MOUSE	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (Growth inhibitory factor) (GIF)	0.06	-	nuc	0		synaptic vesicle [IDA]		1JI9	68
P37361 UniProt NPD GO	MT3_RAT	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (Growth inhibitory factor) (GIF)	0.06	-	nuc	0		synaptic vesicle [ISS]			66
Q40633 UniProt NPD GO	MT1_ORYSA	Metallothionein-like protein 1	0.06	-	nuc	0					74
P20238 UniProt NPD GO	MT1_MIMGU	Metallothionein-like protein 1 (MT-1)	0.06	-	nuc	0					72
Q9VHB6 UniProt NPD GO	MTX1_DROME	Metaxin-1 homolog	0.06	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				327
Q99707 UniProt NPD GO	METH_HUMAN	Methionine synthase (EC 2.1.1.13) (5-methyltetrahydrofolate--homocysteine methyltransferase) (Methio ...	0.06	-	cyt	0	Cytoplasm		250940		1265
P26186 UniProt NPD GO	MGMT_CRIGR	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.06	-	nuc	0	Nucleus (Probable)				209
Q9SE60 UniProt NPD GO	MTHR1_ARATH	Methylenetetrahydrofolate reductase 1 (EC 1.5.1.20) (AtMTHFR1)	0.06	-	cyt	0					592
Q07536 UniProt NPD GO	MMSA_BOVIN	Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27) (MMSDH) ...	0.06	-	mit	1	Mitochondrion	mitochondrion [ISS]			537
P35521 UniProt NPD GO	ICLN_CANFA	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln)) (Chloride channel, ...	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)			1ZYI	235
Q61189 UniProt NPD GO	ICLN_MOUSE	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln)) (Chloride channel, ...	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				236
Q03426 UniProt NPD GO	KIME_HUMAN	Mevalonate kinase (EC 2.7.1.36) (MK)	0.06	-	cyt	0	Cytoplasm. Peroxisome		260920		396
P17256 UniProt NPD GO	KIME_RAT	Mevalonate kinase (EC 2.7.1.36) (MK)	0.06	-	mit	0	Cytoplasm. Peroxisome			1KVK	395
P55083 UniProt NPD GO	MFAP4_HUMAN	Microfibril-associated glycoprotein 4 precursor	0.06	-	exc	0	Secreted protein; extracellular space; extracellular matrix	microfibril [NAS]	600596		255
P79382 UniProt NPD GO	MGST1_PIG	Microsomal glutathione S-transferase 1 (EC 2.5.1.18) (Microsomal GST-1) (Microsomal GST-I)	0.06	-	cyt	3 *	Microsome (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral membrane protein ...				154
P08011 UniProt NPD GO	MGST1_RAT	Microsomal glutathione S-transferase 1 (EC 2.5.1.18) (Microsomal GST-1) (Microsomal GST-I)	0.06	-	mit	3 *	Microsome. Mitochondrion; mitochondrial outer membrane; peripheral membrane protein				154
P67810 UniProt NPD GO	SPC18_BOVIN	Microsomal signal peptidase 18 kDa subunit (EC 3.4.-.-) (SPase 18 kDa subunit) (SPC18) (Endopeptidas ...	0.06	-	nuc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein				179
P67811 UniProt NPD GO	SPC18_CANFA	Microsomal signal peptidase 18 kDa subunit (EC 3.4.-.-) (SPase 18 kDa subunit) (SPC18) (Endopeptidas ...	0.06	-	nuc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein				179
P67812 UniProt NPD GO	SPC18_HUMAN	Microsomal signal peptidase 18 kDa subunit (EC 3.4.-.-) (SPase 18 kDa subunit) (SPC18) (Endopeptidas ...	0.06	-	nuc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein				179
Q5R9C7 UniProt NPD GO	SPC18_PONPY	Microsomal signal peptidase 18 kDa subunit (EC 3.4.-.-) (SPase 18 kDa subunit) (SPC18) (Endopeptidas ...	0.06	-	nuc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				179
P42667 UniProt NPD GO	SPC18_RAT	Microsomal signal peptidase 18 kDa subunit (EC 3.4.-.-) (SPase 18 kDa subunit) (SPC18) (Endopeptidas ...	0.06	-	nuc	2 *	Microsome; microsomal membrane; single-pass type II membrane protein				179
Q9R0P6 UniProt NPD GO	SPC18_MOUSE	Microsomal signal peptidase 18 kDa subunit (EC 3.4.-.-) (SPase 18 kDa subunit) (SPC18) (Endopeptidas ...	0.06	-	nuc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				179
Q6C4R5 UniProt NPD GO	SPC3_YARLI	Microsomal signal peptidase subunit 3 (EC 3.4.-.-)	0.06	-	nuc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				185
Q9D8V0 UniProt NPD GO	HM13_MOUSE	Minor histocompatibility antigen H13 (EC 3.4.99.-) (Signal peptide peptidase) (Presenilin-like prote ...	0.06	+	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA]		1JUF	378
P97700 UniProt NPD GO	M2OM_RAT	Mitochondrial 2-oxoglutarate/malate carrier protein (OGCP) (Solute carrier family 25 member 11)	0.06	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IMP]			313
P46767 UniProt NPD GO	RM14_ACACA	Mitochondrial 60S ribosomal protein L14	0.06	-	cyt	0	Mitochondrion				129
O21256 UniProt NPD GO	RM18_RECAM	Mitochondrial 60S ribosomal protein L18	0.06	-	nuc	0	Mitochondrion				96
Q9H1K4 UniProt NPD GO	GHC2_HUMAN	Mitochondrial glutamate carrier 2 (GC-2) (Glutamate/H(+) symporter 2) (Solute carrier family 25 memb ...	0.06	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)		609303		315
Q3ZBN8 UniProt NPD GO	TIM14_BOVIN	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 19)	0.06	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				115
Q75E80 UniProt NPD GO	TIM22_ASHGO	Mitochondrial import inner membrane translocase subunit TIM22	0.06	-	cyt	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				201
Q99595 UniProt NPD GO	TI17A_HUMAN	Mitochondrial import inner membrane translocase subunit Tim17-A (Inner membrane preprotein transloca ...	0.06	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [TAS] mitochondrial inner membrane presequence tr... [TAS]	605057		171
O35092 UniProt NPD GO	TI17A_RAT	Mitochondrial import inner membrane translocase subunit Tim17-A (Inner membrane preprotein transloca ...	0.06	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane presequence tr... [IPI]			171
O60830 UniProt NPD GO	TI17B_HUMAN	Mitochondrial import inner membrane translocase subunit Tim17-B	0.06	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [TAS] mitochondrial inner membrane presequence tr... [TAS]	300249		172
P87146 UniProt NPD GO	TIM22_SCHPO	Mitochondrial import inner membrane translocase subunit tim22	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				175
P46972 UniProt NPD GO	IMP2_YEAST	Mitochondrial inner membrane protease subunit 2 (EC 3.4.99.-)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane peptidase complex [IDA]			177
Q9N2J1 UniProt NPD GO	UCP2_CANFA	Mitochondrial uncoupling protein 2 (UCP 2)	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				309
O97562 UniProt NPD GO	UCP2_PIG	Mitochondrial uncoupling protein 2 (UCP 2)	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				309
P56500 UniProt NPD GO	UCP2_RAT	Mitochondrial uncoupling protein 2 (UCP 2)	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IPI] mitochondrion [IDA]			309
O77792 UniProt NPD GO	UCP3_BOVIN	Mitochondrial uncoupling protein 3 (UCP 3)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				311
Q9DC61 UniProt NPD GO	MPPA_MOUSE	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				524
P29677 UniProt NPD GO	MPPA_SOLTU	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane				504
Q63538 UniProt NPD GO	MK12_RAT	Mitogen-activated protein kinase 12 (EC 2.7.11.24) (Extracellular signal-regulated kinase 6) (ERK-6) ...	0.06	-	cyt	0	Cytoplasm. Mitochondrion. Mitochondrial when associated with SH3BP5				367
O96007 UniProt NPD GO	MOS2L_HUMAN	Molybdenum cofactor synthesis protein 2 large subunit (Molybdopterin synthase large subunit) (MPT sy ...	0.06	-	nuc	0			603708		188
P02881 UniProt NPD GO	MONA_DIOCU	Monellin chain A (Monellin chain I)	0.06	-	cyt	0				4MON	45
O70324 UniProt NPD GO	MOT8_MOUSE	Monocarboxylate transporter 8 (MCT 8) (X-linked PEST-containing transporter)	0.06	-	end	11	Cell membrane; multi-pass membrane protein (Probable)				565
Q8IY49 UniProt NPD GO	PAQRA_HUMAN	Monocyte to macrophage differentiation factor 2 (Progestin and adipoQ receptor family member X)	0.06	-	end	6	Membrane; multi-pass membrane protein (Potential)				270
Q8R189 UniProt NPD GO	PAQRA_MOUSE	Monocyte to macrophage differentiation factor 2 (Progestin and adipoQ receptor family member X)	0.06	-	end	6	Membrane; multi-pass membrane protein (Potential)				247
Q9Y7N3 UniProt NPD GO	GLRX3_SCHPO	Monothiol glutaredoxin-3	0.06	-	mit	1 *	Nucleus	nuclear envelope-endoplasmic reticulum network [IDA]			166
P15507 UniProt NPD GO	NPMB_BOVIN	Morphine-modulating neuropeptide B	0.06	-		0	Secreted protein				8
Q8BPB0 UniProt NPD GO	MOL1A_MOUSE	Mps one binder kinase activator-like 1A (Mob1 homolog 1A)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			215

You are viewing entries 72501 to 72550 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.