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
Q96WS6 UniProt NPD GO	MEU15_SCHPO	Meiotic expression up-regulated protein 15	0.15	-	cyt	2 *					150
P25453 UniProt NPD GO	DMC1_YEAST	Meiotic recombination protein DMC1	0.15	-	cyt	0	Nucleus	condensed nuclear chromosome [IDA] nucleus [IDA]			334
Q91ZV0 UniProt NPD GO	MIA2_MOUSE	Melanoma inhibitory activity protein 2 precursor	0.15	-	nuc	0	Secreted protein (Potential)				517
P49218 UniProt NPD GO	MTR1A_RAT	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor) (Fragment)	0.15	-	end	3 *	Membrane; multi-pass membrane protein				156
Q9FN18 UniProt NPD GO	NRAM4_ARATH	Metal transporter Nramp4 (AtNramp4)	0.15	-	end	12	Membrane; multi-pass membrane protein (Probable)				512
O97591 UniProt NPD GO	TIMP4_RABIT	Metalloproteinase inhibitor 4 (TIMP-4) (Tissue inhibitor of metalloproteinases 4) (Fragment)	0.15	-	cyt	0	Secreted protein				170
P29499 UniProt NPD GO	MT1_HOMAM	Metallothionein-1 (CuMT-1)	0.15	-	nuc	0				1J5M	58
P02801 UniProt NPD GO	MT1B_HORSE	Metallothionein-1B (MT-1B) (Metallothionein-IB) (MT-IB)	0.15	-	nuc	0					61
P79431 UniProt NPD GO	MT1E_PIG	Metallothionein-1E (MT-1E) (Metallothionein-IE) (MT-IE)	0.15	-	nuc	0					61
P79378 UniProt NPD GO	MT1F_PIG	Metallothionein-1F (MT-1F) (Metallothionein-IF) (MT-IF)	0.15	-	nuc	0					61
P15114 UniProt NPD GO	MT2_CANGA	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II) [Contains: Metallothionein-2' (MT-2') (Metallo ...	0.15	-	nuc	0					51
Q9HFD0 UniProt NPD GO	MT3_YARLI	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (MTPIII)	0.15	-	nuc	0					55
P80410 UniProt NPD GO	MK2B_PALPR	Metalnikowin-2B (Metalnikowin IIB)	0.15	-		0					16
Q9D799 UniProt NPD GO	FMT_MOUSE	Methionyl-tRNA formyltransferase, mitochondrial precursor (EC 2.1.2.9) (MtFMT)	0.15	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			386
Q42777 UniProt NPD GO	MCCA_SOYBN	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4) (3-methylcrotony ...	0.15	-	mit	0	Mitochondrion; mitochondrial matrix				731
Q6AYF7 UniProt NPD GO	MFAP3_RAT	Microfibril-associated glycoprotein 3 precursor	0.15	-	end	2 *	Cell membrane; single-pass type I membrane protein (Potential)				347
P81860 UniProt NPD GO	MIA2_SARMU	Microneme antigen L2 (Lectin SML2)	0.15	-	nuc	0	Microneme				138
Q4QR80 UniProt NPD GO	RT25_RAT	Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25)	0.15	-	cyt	0	Mitochondrion (By similarity)				171
Q03799 UniProt NPD GO	RTS8_YEAST	Mitochondrial 40S ribosomal protein S8	0.15	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IPI]			155
O21033 UniProt NPD GO	RM14_DICDI	Mitochondrial 60S ribosomal protein L14	0.15	-	cyt	0	Mitochondrion	mitochondrial large ribosomal subunit [NAS]			129
P07266 UniProt NPD GO	MRS1_YEAST	Mitochondrial RNA-splicing protein MRS1	0.15	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			363
Q75F72 UniProt NPD GO	TIM13_ASHGO	Mitochondrial import inner membrane translocase subunit TIM13	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				103
Q6CJX3 UniProt NPD GO	TIM13_KLULA	Mitochondrial import inner membrane translocase subunit TIM13	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				101
Q9XH48 UniProt NPD GO	TIM13_ARATH	Mitochondrial import inner membrane translocase subunit Tim13	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				87
Q6DGJ3 UniProt NPD GO	TIM13_BRARE	Mitochondrial import inner membrane translocase subunit Tim13	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q9UT37 UniProt NPD GO	TIM14_SCHPO	Mitochondrial import inner membrane translocase subunit tim14 (Presequence translocated-associated m ...	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				140
Q09783 UniProt NPD GO	TIM8_SCHPO	Mitochondrial import inner membrane translocase subunit tim8	0.15	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				98
Q8X0G8 UniProt NPD GO	MIM1_NEUCR	Mitochondrial import protein 1	0.15	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				130
P82805 UniProt NPD GO	TO204_ARATH	Mitochondrial import receptor subunit TOM20-4 (Translocase of outer membrane 20 kDa subunit 4)	0.15	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				187
P14908 UniProt NPD GO	MTF1_YEAST	Mitochondrial replication protein MTF1 (Mitochondrial transcription factor mtTFB) (RF1023) (Mitochon ...	0.15	-	cyt	0	Mitochondrion	mitochondrial matrix [TAS]		1I4W	340
Q7YEV0 UniProt NPD GO	RMAR_SACSE	Mitochondrial ribosomal protein VAR1	0.15	-	nuc	0	Mitochondrion				269
P11914 UniProt NPD GO	MPPA_YEAST	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.15	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial processing peptidase complex [IDA]		1HR9	482
P50224 UniProt NPD GO	ST1A3_HUMAN	Monoamine-sulfating phenol sulfotransferase (EC 2.8.2.1) (Aryl sulfotransferase 1A3) (Sulfotransfera ...	0.15	-	cyt	0	Cytoplasm	cytoplasm [TAS]	600641	2A3R	295
P80343 UniProt NPD GO	MCPB_BOVIN	Monocyte chemotactic protein 1B (MCP-1B) (Fragment)	0.15	-	mit	0					74
P12872 UniProt NPD GO	MOTI_HUMAN	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.15	-	exc	1 *	Secreted protein	soluble fraction [TAS]	158270	1LBJ	115
Q921Y0 UniProt NPD GO	MOL1B_MOUSE	Mps one binder kinase activator-like 1B (Mob1 homolog 1B)	0.15	-	mit	0					215
Q5RAE0 UniProt NPD GO	MOL1B_PONPY	Mps one binder kinase activator-like 1B (Mob1 homolog 1B)	0.15	-	mit	0					215
Q3T1J9 UniProt NPD GO	MOL1B_RAT	Mps one binder kinase activator-like 1B (Mob1 homolog 1B)	0.15	-	mit	0					215
Q9H8S9 UniProt NPD GO	MOL1B_HUMAN	Mps one binder kinase activator-like 1B (Mob1 homolog 1B) (Mob1 alpha) (Mob1A) (Protein Mob4B)	0.15	-	mit	0				1PI1	215
P21441 UniProt NPD GO	MDR_LEITA	Multidrug resistance protein (EC 3.6.3.44) (P-glycoprotein)	0.15	-	end	9	Membrane; multi-pass membrane protein				1548
Q9FWX8 UniProt NPD GO	MDR16_ARATH	Multidrug resistance protein 16 (P-glycoprotein 12)	0.15	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1229
Q8HXQ5 UniProt NPD GO	MRP1_BOVIN	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.15	-	end	14 *	Membrane; multi-pass membrane protein (By similarity)				1530
P41985 UniProt NPD GO	ACM2_BOVIN	Muscarinic acetylcholine receptor M2	0.15	-	end	7 *	Membrane; multi-pass membrane protein				465
P10980 UniProt NPD GO	ACM2_RAT	Muscarinic acetylcholine receptor M2	0.15	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			466
O95297 UniProt NPD GO	MPZL1_HUMAN	Myelin protein zero-like protein 1 precursor (Protein zero-related)	0.15	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	604376		269
P87110 UniProt NPD GO	ITR2_SCHPO	Myo-inositol transporter 2	0.15	-	end	10	Membrane; multi-pass membrane protein				557
P52179 UniProt NPD GO	MYOM1_HUMAN	Myomesin-1 (190 kDa titin-associated protein) (190 kDa connectin-associated protein)	0.15	-	cyt	0		striated muscle thick filament [TAS]	603508		1451
Q9QVP4 UniProt NPD GO	MLRA_MOUSE	Myosin regulatory light chain 2, atrial isoform (Myosin light chain 2a) (MLC-2a) (MLC2a) (Myosin reg ...	0.15	-	mit	0		myosin [ISS]			175
P04466 UniProt NPD GO	MLRS_RAT	Myosin regulatory light chain 2, skeletal muscle isoform (G2) (DTNB) (MLC-2)	0.15	+	cyt	0					168
P24732 UniProt NPD GO	MLRT_RABIT	Myosin regulatory light chain 2, skeletal muscle isoform type 1 (G2) (DTNB) (MLC-2)	0.15	+	cyt	0					169

You are viewing entries 57201 to 57250 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.