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
P01655 UniProt NPD GO	KV3B_MOUSE	Ig kappa chain V-III region PC 7132	0.16	-	nuc	0					112
P01671 UniProt NPD GO	KV3S_MOUSE	Ig kappa chain V-III region PC 7175	0.16	-	mit	0					111
P01666 UniProt NPD GO	KV3N_MOUSE	Ig kappa chain V-III region PC 7183	0.16	-	nuc	0					111
P01680 UniProt NPD GO	KV4A_MOUSE	Ig kappa chain V-IV region S107B precursor	0.16	-	nuc	0					129
P01839 UniProt NPD GO	KACB_RABIT	Ig kappa-b4 chain C region	0.16	-	nuc	0					106
P01838 UniProt NPD GO	KAC9_RABIT	Ig kappa-b9 chain C region	0.16	-	nuc	0					104
P01715 UniProt NPD GO	LV4A_HUMAN	Ig lambda chain V-IV region Bau	0.16	-	nuc	0		extracellular region [NAS]			106
P01716 UniProt NPD GO	LV4B_HUMAN	Ig lambda chain V-IV region X	0.16	-	nuc	0		extracellular region [NAS]			106
Q8ML70 UniProt NPD GO	IM10_DROME	Immune-induced peptides precursor [Contains: Immune-induced peptide 10 (DIM-10); Immune-induced pept ...	0.16	-	cyt	0	Secreted protein	extracellular region [IDA]			268
Q9FYP9 UniProt NPD GO	IMA2_ORYSA	Importin alpha-2 subunit	0.16	-	cyt	0	Cytoplasm; perinuclear region				528
Q8HYS5 UniProt NPD GO	MCL1_CANFA	Induced myeloid leukemia cell differentiation protein Mcl-1 homolog	0.16	-	nuc	1	Membrane; single-pass membrane protein (By similarity). Cytoplasm (By similarity). Mitochondrion (By ...	cytoplasm [ISS] mitochondrial outer membrane [ISS]			350
Q58DF9 UniProt NPD GO	ICOS_BOVIN	Inducible T-cell co-stimulator precursor (CD278 antigen)	0.16	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				209
P81907 UniProt NPD GO	ISP3_GALME	Inducible serine protease inhibitor 3 (ISPI-3) (Fragment)	0.16	-	nuc	0					41
Q9UTR6 UniProt NPD GO	OCH1_SCHPO	Initiation-specific alpha-1,6-mannosyltransferase (EC 2.4.1.232)	0.16	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				396
O43092 UniProt NPD GO	OXA12_SCHPO	Inner membrane protein oxa1-2, mitochondrial precursor (Cytochrome oxidase biogenesis protein 1-2) ( ...	0.16	-	nuc	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [TAS]			409
Q9ZWT3 UniProt NPD GO	PHT16_ARATH	Inorganic phosphate transporter 1-6 (AtPht1;6) (H(+)/Pi cotransporter)	0.16	-	end	10 *	Cell membrane; multi-pass membrane protein (By similarity)				516
Q3SWY3 UniProt NPD GO	IMDH2_BOVIN	Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) (IMP dehydrogenase 2) (IMPDH-II) (IMPD 2)	0.16	-	cyt	0					514
Q7TT16 UniProt NPD GO	IPMK_MOUSE	Inositol polyphosphate multikinase (EC 2.7.1.151) (Inositol 1,3,4,6-tetrakisphosphate 5-kinase)	0.16	-	cyt	0	Nucleus (By similarity)				396
Q6UW32 UniProt NPD GO	IGFL1_HUMAN	Insulin growth factor-like family member 1 precursor	0.16	-	exc	1 *	Secreted protein (Probable)				110
Q6JLX1 UniProt NPD GO	IGF1_AILME	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.16	-	nuc	0	Secreted protein				153
P33712 UniProt NPD GO	IGF1_CANFA	Insulin-like growth factor I precursor (IGF-I) (Somatomedin) (Fragment)	0.16	-	exc	0	Secreted protein				122
P51462 UniProt NPD GO	IGF1_COTJA	Insulin-like growth factor I precursor (IGF-I) (Somatomedin) (Fragment)	0.16	-	exc	0	Secreted protein				124
P13384 UniProt NPD GO	IBP2_BOVIN	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.16	-	exc	1 *	Secreted protein				317
P35859 UniProt NPD GO	ALS_RAT	Insulin-like growth factor-binding protein complex acid labile chain precursor (ALS)	0.16	-	nuc	0	Secreted protein; extracellular space				603
Q18936 UniProt NPD GO	U359_CAEEL	Integral membrane UPF0359 protein D1046.5	0.16	+	end	7	Membrane; multi-pass membrane protein (By similarity)				458
P61625 UniProt NPD GO	ITAL_BOVIN	Integrin alpha-L precursor (Leukocyte adhesion glycoprotein LFA-1 alpha chain) (LFA-1A) (Leukocyte f ...	0.16	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				1165
P11578 UniProt NPD GO	ITAM_CAVPO	Integrin alpha-M (Cell surface glycoprotein MAC-1 subunit alpha) (CR-3 alpha chain) (Leukocyte adhes ...	0.16	-	cyt	0	Membrane; single-pass type I membrane protein				126
Q9R002 UniProt NPD GO	II2B_MOUSE	Interferon-activable protein 202b (Ifi-202b) (Interferon-inducible protein p202b)	0.16	-	nuc	0	Cytoplasm. Nucleus. Accumulates first in the cytoplasm, and is translocated to the nucleus after a d ...				445
Q5RFJ1 UniProt NPD GO	ILF2_PONPY	Interleukin enhancer-binding factor 2	0.16	-	mit	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS] nucleus [ISS]			390
Q12905 UniProt NPD GO	ILF2_HUMAN	Interleukin enhancer-binding factor 2 (Nuclear factor of activated T-cells 45 kDa)	0.16	-	mit	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]	603181		390
Q9CXY6 UniProt NPD GO	ILF2_MOUSE	Interleukin enhancer-binding factor 2 (Nuclear factor of activated T-cells 45 kDa)	0.16	-	mit	0	Nucleus; nucleolus	nucleolus [ISS] nucleus [ISS]			390
Q9UHA7 UniProt NPD GO	IL1F6_HUMAN	Interleukin-1 family member 6 (IL-1F6) (Interleukin-1 epsilon) (IL-1 epsilon) (FIL1 epsilon)	0.16	-	cyt	0	Secreted protein (Potential)	extracellular region [NAS]	605509		158
Q29056 UniProt NPD GO	IL1RA_PIG	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.16	-	end	0	Secreted protein (By similarity)				177
Q28268 UniProt NPD GO	IL12B_CANFA	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.16	-	gol	1 *	Secreted protein	extracellular space [ISS]			329
O70394 UniProt NPD GO	I27RA_MOUSE	Interleukin-27 receptor alpha chain precursor (IL-27R-alpha) (WSX-1) (Type I T-cell cytokine recepto ...	0.16	-	nuc	0	Membrane; single-pass type I membrane protein				623
Q865X5 UniProt NPD GO	IL4_LAMGL	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.16	-	nuc	0	Secreted protein				133
P21692 UniProt NPD GO	MMP1_PIG	Interstitial collagenase precursor (EC 3.4.24.7) (Matrix metalloproteinase-1) (MMP-1) [Contains: 18 ...	0.16	-	exc	0				1FBL	469
P35561 UniProt NPD GO	IRK2_MOUSE	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.16	-	end	2	Membrane; multi-pass membrane protein			1U4F	428
O18839 UniProt NPD GO	IRK2_PIG	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.16	-	mit	2	Membrane; multi-pass membrane protein				427
O19182 UniProt NPD GO	IRK2_BOVIN	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.16	-	mit	2	Membrane; multi-pass membrane protein				427
Q9MYY9 UniProt NPD GO	IRK2_CANFA	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.16	-	mit	2	Membrane; multi-pass membrane protein				427
P52185 UniProt NPD GO	IRK2_CAVPO	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.16	-	mit	2	Membrane; multi-pass membrane protein				427
P52186 UniProt NPD GO	IRK2_CHICK	Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying subfamily J member 2) ( ...	0.16	-	mit	2	Membrane; multi-pass membrane protein				427
P10997 UniProt NPD GO	IAPP_HUMAN	Islet amyloid polypeptide precursor (Diabetes-associated peptide) (DAP) (Amylin) (Insulinoma amyloid ...	0.16	-	nuc	0	Secreted protein	soluble fraction [TAS]	147940		89
Q4R4W5 UniProt NPD GO	IDI1_MACFA	Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) (IPP isomerase 1) (Isopentenyl pyrophosphate ...	0.16	-	cyt	0	Peroxisome (By similarity)				227
Q5R8R6 UniProt NPD GO	IDI1_PONPY	Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) (IPP isomerase 1) (Isopentenyl pyrophosphate ...	0.16	-	cyt	0	Peroxisome (By similarity)				227
Q6H321 UniProt NPD GO	KLK2_HORSE	Kallikrein-1E2 precursor (EC 3.4.21.35) (Glandular kallikrein) (HPK)	0.16	-	mit	0	Secreted protein			1GVZ	261
Q95147 UniProt NPD GO	CASK_CERDU	Kappa-casein (Fragment)	0.16	-	nuc	0	Secreted protein				122
Q95227 UniProt NPD GO	CASK_OVIMO	Kappa-casein (Fragment)	0.16	-	nuc	0	Secreted protein				124
P07498 UniProt NPD GO	CASK_HUMAN	Kappa-casein precursor	0.16	-	nuc	0	Secreted protein	extracellular region [NAS]	601695		182

You are viewing entries 55801 to 55850 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.