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
P48101 UniProt NPD GO	CHLI_CYAPA	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.18	-	cyt	0	Plastid; cyanelle				347
Q86V88 UniProt NPD GO	MGDP1_HUMAN	Magnesium-dependent phosphatase 1 (EC 3.1.3.-) (EC 3.1.3.48) (MDP-1)	0.18	-	cyt	0					176
P40242 UniProt NPD GO	PRIO1_TRAST	Major prion protein 1 precursor (PrP) (Major scrapie-associated fibril protein 1) (CD230 antigen)	0.18	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor				264
Q6EH52 UniProt NPD GO	PRIO_AILME	Major prion protein precursor (PrP) (CD230 antigen)	0.18	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
Q5UJG7 UniProt NPD GO	PRIO_BOSTR	Major prion protein precursor (PrP) (CD230 antigen)	0.18	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
O46501 UniProt NPD GO	PRIO_CANFA	Major prion protein precursor (PrP) (CD230 antigen)	0.18	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor			1XYK	255
P23907 UniProt NPD GO	PRIO_SHEEP	Major prion protein precursor (PrP) (CD230 antigen)	0.18	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor			1Y2S	256
P40247 UniProt NPD GO	PRIO_CALJA	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				252
P67988 UniProt NPD GO	PRIO_CERAE	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				245
P67989 UniProt NPD GO	PRIO_CERDI	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				245
P40251 UniProt NPD GO	PRIO_COLGU	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				253
P67993 UniProt NPD GO	PRIO_MACAR	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				253
P67992 UniProt NPD GO	PRIO_MACFA	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				253
P67994 UniProt NPD GO	PRIO_MACFU	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				253
P67997 UniProt NPD GO	PRIO_MACMU	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				253
P67995 UniProt NPD GO	PRIO_MACNE	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				253
P67996 UniProt NPD GO	PRIO_PAPHA	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				253
P40257 UniProt NPD GO	PRIO_PREFR	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.18	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				253
Q94053 UniProt NPD GO	MSP78_CAEEL	Major sperm protein 78 (MSP)	0.18	-	cyt	0					126
Q42686 UniProt NPD GO	MDHM_CHLRE	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.18	-	mit	0	Mitochondrion; mitochondrial matrix				373
P13244 UniProt NPD GO	MASY_BRANA	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.18	-	cyt	0	Glyoxysome				561
P28345 UniProt NPD GO	MASY_NEUCR	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.18	-	pox	0	Glyoxysome				542
Q8IVS2 UniProt NPD GO	FABD_HUMAN	Malonyl CoA-acyl carrier protein transacylase, mitochondrial precursor (EC 2.3.1.39) (MCT) (Mitochon ...	0.18	-	mit	0	Mitochondrion	mitochondrion [IDA]		2C2N	390
Q7XTQ5 UniProt NPD GO	MEX1_ORYSA	Maltose excess protein 1-like, chloroplast precursor	0.18	-	end	8	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				399
O95460 UniProt NPD GO	MATN4_HUMAN	Matrilin-4 precursor	0.18	-	cyt	0	Secreted protein	extracellular region [TAS]	603897		622
Q58T55 UniProt NPD GO	M9H3_BOMMX	Maximins 9/H3 precursor [Contains: Maximin-9; Maximin-H3]	0.18	-	end	0	Secreted protein				144
O01811 UniProt NPD GO	MEC6_CAEEL	Mechanosensory abnormality protein 6	0.18	-	mit	1 *	Membrane; multi-pass membrane protein				377
P83418 UniProt NPD GO	MRN2_MEGVI	Megourin-2	0.18	-	nuc	0	Secreted protein				63
Q8CIQ6 UniProt NPD GO	MTR1B_MOUSE	Melatonin receptor type 1B (Mel-1B-R) (Mel1b melatonin receptor)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				364
Q28558 UniProt NPD GO	MTR1L_SHEEP	Melatonin-related receptor (G protein-coupled receptor 50) (H9)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				575
P59261 UniProt NPD GO	MEL_POLHE	Melittin precursor	0.18	-	end	2 *	Secreted protein (By similarity)				70
P59262 UniProt NPD GO	MEL_VESMC	Melittin precursor	0.18	-	exc	2 *	Secreted protein (By similarity)				70
P68408 UniProt NPD GO	MEL_VESMG	Melittin precursor	0.18	-	exc	2 *	Secreted protein (By similarity)				70
P68409 UniProt NPD GO	MEL_VESVN	Melittin precursor	0.18	-	exc	2 *	Secreted protein (By similarity)				70
P01501 UniProt NPD GO	MEL_APIME	Melittin precursor (Allergen Api m 3) (Api m III)	0.18	-	exc	2 *	Secreted protein			2MLT	70
Q8VHK5 UniProt NPD GO	MLC1_MOUSE	Membrane protein MLC1	0.18	-	end	7	Membrane; multi-pass membrane protein (Potential)				382
P49061 UniProt NPD GO	TIMP1_PAPCY	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.18	-	nuc	0	Secreted protein				207
P20614 UniProt NPD GO	TIMP1_RABIT	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.18	-	end	0	Secreted protein				207
P55952 UniProt NPD GO	MT_POTPO	Metallothionein (MT)	0.18	-	nuc	0					58
P79380 UniProt NPD GO	MT2B_PIG	Metallothionein-2B (MT-2B) (Metallothionein-IIB) (MT-IIB)	0.18	-	nuc	0					61
P80408 UniProt NPD GO	MK1_PALPR	Metalnikowin-1 (Metalnikowin I)	0.18	-		0					15
P80409 UniProt NPD GO	MK2A_PALPR	Metalnikowin-2A (Metalnikowin IIA)	0.18	-		0					15
P80411 UniProt NPD GO	MK3_PALPR	Metalnikowin-3 (Metalnikowin III)	0.18	-		0					16
Q6CRY8 UniProt NPD GO	SCP3_KLULA	Microsomal signal peptidase subunit 3 (EC 3.4.-.-)	0.18	-	exc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				189
Q9CQ20 UniProt NPD GO	M1IP1_MOUSE	Mid1-interacting protein 1 (Gastrulation-specific G12-like protein) (Mid1-interacting G12-like prote ...	0.18	-	nuc	0	Nucleus. Cytoplasm. Associated with microtubules	microtubule cytoskeleton [IDA]			182
O21235 UniProt NPD GO	RM01_RECAM	Mitochondrial 60S ribosomal protein L1	0.18	-	nuc	0	Mitochondrion				224
P51409 UniProt NPD GO	RM05_SOLTU	Mitochondrial 60S ribosomal protein L5	0.18	-	cyt	0	Mitochondrion				186
P10566 UniProt NPD GO	MRS3_YEAST	Mitochondrial RNA-splicing protein MRS3	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			314
Q8JZN7 UniProt NPD GO	MIRO2_MOUSE	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.18	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)	mitochondrial inner membrane [IDA]			620
Q864R5 UniProt NPD GO	MIRO2_PIG	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.18	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				620

You are viewing entries 53251 to 53300 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.