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
Q9JLA2 UniProt NPD GO	IL1F6_MOUSE	Interleukin-1 family member 6 (IL-1F6) (Interleukin-1 epsilon) (IL-1 epsilon) (FIL1 epsilon) (Interl ...	0.09	-	cyt	0	Secreted protein (Potential)				160
Q866R8 UniProt NPD GO	IL1RA_MACFA	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.09	-	end	0	Secreted protein				177
Q62929 UniProt NPD GO	ILRL2_RAT	Interleukin-1 receptor-like 2 precursor (Interleukin-1 receptor-related protein 2) (IL1R-rp2)	0.09	-	end	1 *	Membrane; single-pass type I membrane protein				561
Q01344 UniProt NPD GO	IL5RA_HUMAN	Interleukin-5 receptor alpha chain precursor (IL-5R-alpha) (CD125 antigen) (CDw125)	0.09	-	end	1	Membrane; single-pass type I membrane protein	extracellular space [TAS] integral to membrane [TAS]	147851	1OBX	420
P0C1D2 UniProt NPD GO	MIA40_EMENI	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				283
P09923 UniProt NPD GO	PPBI_HUMAN	Intestinal alkaline phosphatase precursor (EC 3.1.3.1) (IAP)	0.09	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [NAS]	171740		528
P03879 UniProt NPD GO	MBI4_YEAST	Intron-encoded RNA maturase bI4 precursor (RNA maturase SCbI4) [Contains: Truncated, nonfunctional c ...	0.09	-	end	7 *	Mitochondrion	mitochondrion [IDA]			638
Q6BJW6 UniProt NPD GO	INV_DEBHA	Invertase precursor (EC 3.2.1.26) (Beta-fructofuranosidase) (Saccharase)	0.09	-	exc	0					534
Q6FJY3 UniProt NPD GO	ISU1_CANGA	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.09	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				213
Q4R502 UniProt NPD GO	IDHP_MACFA	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.09	-	mit	0	Mitochondrion (By similarity)				452
P28834 UniProt NPD GO	IDH1_YEAST	Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.09	-	mit	0	Mitochondrion	mitochondrial nucleoid [IDA]			360
Q42553 UniProt NPD GO	IDI2_ARATH	Isopentenyl-diphosphate delta-isomerase II (EC 5.3.3.2) (IPP isomerase II) (Isopentenyl pyrophosphat ...	0.09	-	mit	0					284
P82226 UniProt NPD GO	TJT1B_HADVE	Janus-atracotoxin-Hv1b (J-AcTx-Hv1b)	0.09	-	nuc	0	Secreted protein				36
P82228 UniProt NPD GO	TJT1C_HADVE	Janus-atracotoxin-Hv1c (J-AcTx-Hv1c)	0.09	-	nuc	0	Secreted protein			1DL0	37
Q9JI59 UniProt NPD GO	JAM2_MOUSE	Junctional adhesion molecule B precursor (JAM-B) (Junctional adhesion molecule 2) (Vascular endothel ...	0.09	-	end	1	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein. Localized at ...				298
Q86YT9 UniProt NPD GO	JAML1_HUMAN	Junctional adhesion molecule-like precursor (Dendritic cell-specific protein CREA7-1) (Adhesion mole ...	0.09	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Localized at the plasma memb ...		609770		394
P15500 UniProt NPD GO	JHBP_MANSE	Juvenile hormone-binding protein precursor (Fragment)	0.09	-	cyt	0	Secreted protein				229
Q9NVX7 UniProt NPD GO	KBTB4_HUMAN	Kelch repeat and BTB domain-containing protein 4 (BTB and kelch domain-containing protein 4)	0.09	-	cyt	0					518
Q8IUB9 UniProt NPD GO	KR191_HUMAN	Keratin-associated protein 19-1 (High tyrosine-glycine keratin-associated protein 19.1)	0.09	-	cyt	2 *					90
Q3LI73 UniProt NPD GO	KR194_HUMAN	Keratin-associated protein 19-4	0.09	-	cyt	1 *					84
Q3LI72 UniProt NPD GO	KR195_HUMAN	Keratin-associated protein 19-5	0.09	-	cyt	0					72
P02446 UniProt NPD GO	KRA31_SHEEP	Keratin-associated protein 3-1 (Keratin, high sulfur matrix protein, IIIB2)	0.09	-	nuc	0					97
Q5D0X0 UniProt NPD GO	FGF7_CEREL	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.09	-	mit	0	Secreted protein				194
P36363 UniProt NPD GO	FGF7_MOUSE	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.09	-	mit	0	Secreted protein	extracellular region [IDA] Golgi apparatus [IDA]			194
Q9N198 UniProt NPD GO	FGF7_PIG	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.09	-	mit	0	Secreted protein (By similarity)				194
Q53RY4 UniProt NPD GO	KCP3_HUMAN	Keratinocytes-associated protein 3 (KCP-3)	0.09	-	end	3 *	Membrane; multi-pass membrane protein				240
P38674 UniProt NPD GO	ILV5_NEUCR	Ketol-acid reductoisomerase, mitochondrial precursor (EC 1.1.1.86) (Acetohydroxy-acid reductoisomera ...	0.09	-	mit	0	Mitochondrion				402
Q8K274 UniProt NPD GO	KT3K_MOUSE	Ketosamine-3-kinase (EC 2.7.1.-) (Fructosamine-3-kinase-related protein)	0.09	-	cyt	0					309
Q8N743 UniProt NPD GO	KI3L3_HUMAN	Killer cell immunoglobulin-like receptor 3DL3 precursor (Killer cell inhibitory receptor 1) (CD158z ...	0.09	-	end	1	Membrane; single-pass type I membrane protein				410
Q96MU8 UniProt NPD GO	KREM1_HUMAN	Kremen protein 1 precursor (Kringle-containing protein marking the eye and the nose) (Kringle domain ...	0.09	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS] membrane fraction [TAS]	609898		475
P83606 UniProt NPD GO	BMTI6_BOOMI	Kunitz-type serine protease inhibitor BmTI-6 (Fragment)	0.09	-	nuc	0	Secreted protein				35
Q16719 UniProt NPD GO	KYNU_HUMAN	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.09	-	cyt	0	Cytoplasm		605197		465
Q91YP0 UniProt NPD GO	L2HDH_MOUSE	L-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.2) (Duranin)	0.09	-	mit	0	Mitochondrion (By similarity)	integral to membrane [ISS] integral to mitochondrial inner membrane [ISS] mitochondrion [ISS]			464
Q5R9N7 UniProt NPD GO	L2HDH_PONPY	L-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.2) (Duranin)	0.09	-	nuc	0	Mitochondrion (Potential)				419
Q96RQ9 UniProt NPD GO	OXLA_HUMAN	L-amino-acid oxidase precursor (EC 1.4.3.2) (LAAO) (Interleukin-4-induced protein 1) (IL4-induced pr ...	0.09	-	end	0	Isoform 1, isoform 2: Lysosome (By similarity)		609742		567
Q43534 UniProt NPD GO	LIM2_LILLO	LIM2 protein precursor	0.09	-	exc	0					90
Q6UWM7 UniProt NPD GO	LCTL_HUMAN	Lactase-like protein precursor (Klotho/lactase-phlorizin hydrolase-related protein)	0.09	-	exc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				567
Q99KP3 UniProt NPD GO	CRYL1_MOUSE	Lambda-crystallin homolog	0.09	-	cyt	0					318
Q10231 UniProt NPD GO	ERG7_SCHPO	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.09	-	cyt	0					721
Q8BSM7 UniProt NPD GO	LAT3_MOUSE	Large neutral amino acids transporter small subunit 3 (L-type amino acid transporter 3) (Solute carr ...	0.09	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [ISS]			564
P83410 UniProt NPD GO	LEC_ERYCG	Lectin (ECL)	0.09	-	cyt	0				1GZ9	239
Q944P7 UniProt NPD GO	AMPL3_ARATH	Leucine aminopeptidase 3, chloroplast precursor (EC 3.4.11.1) (LAP 3) (Leucyl aminopeptidase 3) (Pro ...	0.09	-	mit	0	Plastid; chloroplast (Potential)				583
Q27956 UniProt NPD GO	LIF_BOVIN	Leukemia inhibitory factor precursor (LIF)	0.09	-	mit	0	Secreted protein				202
O62728 UniProt NPD GO	LIF_MUSVI	Leukemia inhibitory factor precursor (LIF)	0.09	-	mit	0	Secreted protein				202
P31838 UniProt NPD GO	LIGB_PHACH	Ligninase B precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.09	-	exc	0					372
P32949 UniProt NPD GO	LIP5_CANRU	Lipase 5 precursor (EC 3.1.1.3)	0.09	-	exc	0					549
P19515 UniProt NPD GO	LIP_RHIMI	Lipase precursor (EC 3.1.1.3) (Triacylglycerol lipase)	0.09	-	exc	1 *				5TGL	363
P11152 UniProt NPD GO	LIPL_MOUSE	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.09	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				474
Q06327 UniProt NPD GO	LOX1_ARATH	Lipoxygenase 1 (EC 1.13.11.12)	0.09	-	cyt	0	Cytoplasm				859
P41490 UniProt NPD GO	LMT4_LOCMI	Locustamyotropin-4 (Lom-MT-4)	0.09	-		0	Secreted protein				13

You are viewing entries 66401 to 66450 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.