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
Q99N09 UniProt NPD GO	M4A6B_MOUSE	Membrane-spanning 4-domains subfamily A member 6B	0.09	-	end	4 *	Membrane; multi-pass membrane protein				244
Q9TTY1 UniProt NPD GO	TIMP2_CANFA	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2)	0.09	-	exc	0	Secreted protein				220
P84865 UniProt NPD GO	MT1_NECLU	Metallothionein	0.09	-	nuc	0					24
Q7ZZP9 UniProt NPD GO	MT_OREAU	Metallothionein (MT)	0.09	-	nuc	0					60
Q6S4N8 UniProt NPD GO	MT_ORYLA	Metallothionein (MT)	0.09	-	nuc	0					60
P55945 UniProt NPD GO	MT_PSEAM	Metallothionein (MT)	0.09	-	nuc	0					60
P80248 UniProt NPD GO	MT13_MYTED	Metallothionein 10-III (MT-10-III)	0.09	-	nuc	0					72
O19000 UniProt NPD GO	MT1_CANFA	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.09	-	nuc	0					61
P80294 UniProt NPD GO	MT1H_HUMAN	Metallothionein-1H (MT-1H) (Metallothionein-IH) (MT-IH) (Metallothionein-0) (MT-0)	0.09	-	nuc	0			156354		61
Q93083 UniProt NPD GO	MT1L_HUMAN	Metallothionein-1L (MT-1L) (Metallothionein-IL) (MT-IL)	0.09	-	nuc	0		cytoplasm [NAS]	156358		61
P41928 UniProt NPD GO	MT2_YARLI	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.09	-	nuc	0					54
Q9HFC9 UniProt NPD GO	MT4_YARLI	Metallothionein-4 (MT-4) (Metallothionein-IV) (MT-IV) (MTPIV)	0.09	-	nuc	0					54
P20830 UniProt NPD GO	MT1_PEA	Metallothionein-like protein 1 (MT-1)	0.09	-	nuc	0					75
P43392 UniProt NPD GO	MT1A_ARATH	Metallothionein-like protein 1A (MT-1A) (MT-Q) (MT-2)	0.09	-	nuc	0					45
Q9FV51 UniProt NPD GO	AMP1C_ARATH	Methionine aminopeptidase 1C, chloroplast/mitochondrial precursor (EC 3.4.11.18) (MetAP 1C) (MAP 1C) ...	0.09	-	cyt	0	Plastid; chloroplast. Mitochondrion				344
Q9SE94 UniProt NPD GO	MTHR1_MAIZE	Methylenetetrahydrofolate reductase 1 (EC 1.5.1.20) (ZmMTHFR1)	0.09	-	cyt	0					593
Q5ZL21 UniProt NPD GO	MMAC_CHICK	Methylmalonic aciduria and homocystinuria type C homolog	0.09	-	cyt	0					238
Q61166 UniProt NPD GO	MARE1_MOUSE	Microtubule-associated protein RP/EB family member 1 (APC-binding protein EB1) (End-binding protein ...	0.09	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network at the growing distal tip of micr ...	Golgi apparatus [IDA] microtubule [IDA]			267
Q9R1S9 UniProt NPD GO	MK_RAT	Midkine precursor (MK)	0.09	+	nuc	1 *	Secreted protein (Probable)	extracellular space [ISS]			140
P12025 UniProt NPD GO	MK_MOUSE	Midkine precursor (MK) (Retinoic acid-induced differentiation factor)	0.09	-	nuc	1 *	Secreted protein (Probable)				140
P24052 UniProt NPD GO	MK_CHICK	Midkine precursor (Retinoic acid-induced heparin-binding protein) (RI-HB)	0.09	+	nuc	1 *	Cell surface. Secreted protein; extracellular space; extracellular matrix; basement membrane. Baseme ...				142
O18874 UniProt NPD GO	ALL2_CANFA	Minor allergen Can f 2 precursor (Allergen Dog 2)	0.09	-	exc	0	Secreted protein				180
P49276 UniProt NPD GO	DERF6_DERFA	Mite allergen Der f 6 precursor (EC 3.4.21.-) (Der f VI) (DF5)	0.09	-	mit	0	Secreted protein				279
P82649 UniProt NPD GO	RT22_BOVIN	Mitochondrial 28S ribosomal protein S22 (S22mt) (MRP-S22) (Fragments)	0.09	-	cyt	0	Mitochondrion				54
P46766 UniProt NPD GO	RM11_ACACA	Mitochondrial 60S ribosomal protein L11	0.09	-	cyt	0	Mitochondrion				339
P46748 UniProt NPD GO	RM06_PROWI	Mitochondrial 60S ribosomal protein L6	0.09	-	nuc	0	Mitochondrion				194
Q8BL03 UniProt NPD GO	MCATL_MOUSE	Mitochondrial carnitine/acylcarnitine carrier protein CACL (CACT-like) (Solute carrier family 25 mem ...	0.09	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			306
Q5NVC1 UniProt NPD GO	DNC_PONPY	Mitochondrial deoxynucleotide carrier (Solute carrier family 25 member 19)	0.09	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				320
Q9QZD8 UniProt NPD GO	DIC_MOUSE	Mitochondrial dicarboxylate carrier (Solute carrier family 25 member 10)	0.09	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			287
Q9DB41 UniProt NPD GO	GHC2_MOUSE	Mitochondrial glutamate carrier 2 (GC-2) (Glutamate/H(+) symporter 2) (Solute carrier family 25 memb ...	0.09	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			312
Q75BZ1 UniProt NPD GO	PPT2_ASHGO	Mitochondrial holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) (Mitochondrial holo-ACP synthase) (4 ...	0.09	-	nuc	0	Mitochondrion (By similarity)				174
P32830 UniProt NPD GO	TIM12_YEAST	Mitochondrial import inner membrane translocase subunit TIM12 (Mitochondrial regulator of splicing 5 ...	0.09	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein	mitochondrial inner membrane protein insert... [TAS] mitochondrial intermembrane space [TAS]			109
Q6PBT7 UniProt NPD GO	TIM14_BRARE	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 19)	0.09	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				115
Q9P335 UniProt NPD GO	TIM10_PICFA	Mitochondrial import inner membrane translocase subunit Tim10	0.09	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				90
Q6GPY0 UniProt NPD GO	TI13A_XENLA	Mitochondrial import inner membrane translocase subunit Tim13 A	0.09	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				96
Q9C0N3 UniProt NPD GO	TIM10_NEUCR	Mitochondrial import inner membrane translocase subunit tim-10	0.09	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				90
Q5B187 UniProt NPD GO	TIM16_EMENI	Mitochondrial import inner membrane translocase subunit tim16 (Presequence translocated-associated m ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				135
Q2KHZ4 UniProt NPD GO	MIA40_BOVIN	Mitochondrial intermembrane space import and assembly protein 40 (Coiled-coil-helix-coiled-coil-heli ...	0.09	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				137
Q5BJN5 UniProt NPD GO	MIA40_RAT	Mitochondrial intermembrane space import and assembly protein 40 (Coiled-coil-helix-coiled-coil-heli ...	0.09	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				139
Q02608 UniProt NPD GO	RT16_YEAST	Mitochondrial ribosomal protein S16	0.09	-	mit	0	Mitochondrion (Probable)	mitochondrial small ribosomal subunit [IPI]			121
O95847 UniProt NPD GO	UCP4_HUMAN	Mitochondrial uncoupling protein 4 (UCP 4) (Solute carrier family 25 member 27)	0.09	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS] mitochondrion [TAS]			323
Q10713 UniProt NPD GO	MPPA_HUMAN	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.09	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [TAS]			525
O60669 UniProt NPD GO	MOT2_HUMAN	Monocarboxylate transporter 2 (MCT 2)	0.09	-	end	11 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603654		478
O15374 UniProt NPD GO	MOT5_HUMAN	Monocarboxylate transporter 5 (MCT 5) (MCT 4)	0.09	-	end	12 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603878		487
O15375 UniProt NPD GO	MOT6_HUMAN	Monocarboxylate transporter 6 (MCT 6) (MCT 5)	0.09	-	end	12 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603879		505
P08571 UniProt NPD GO	CD14_HUMAN	Monocyte differentiation antigen CD14 precursor (Myeloid cell-specific leucine-rich glycoprotein) [C ...	0.09	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	plasma membrane [TAS]	158120		375
P79350 UniProt NPD GO	OPRM_BOVIN	Mu-type opioid receptor (MOR-1)	0.09	-	end	7	Membrane; multi-pass membrane protein				401
P35372 UniProt NPD GO	OPRM_HUMAN	Mu-type opioid receptor (MOR-1)	0.09	-	end	7	Membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] Golgi apparatus [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	600018		400
Q9WVM7 UniProt NPD GO	MCA2_CRIGR	Multisynthetase complex auxiliary component p38	0.09	-	cyt	0					320
P10522 UniProt NPD GO	MYP0_BOVIN	Myelin P0 protein (Myelin protein zero) (Myelin peripheral protein) (MPP)	0.09	-	nuc	1	Membrane; single-pass type I membrane protein				219

You are viewing entries 66501 to 66550 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.