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
Q6CLJ5 UniProt NPD GO	MRS2_KLULA	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.11	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				442
Q23027 UniProt NPD GO	INX5_CAEEL	Innexin-5	0.11	-	vac	3 *	Membrane; multi-pass membrane protein				447
P28239 UniProt NPD GO	IPYR2_YEAST	Inorganic pyrophosphatase, mitochondrial precursor (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (P ...	0.11	-	mit	0	Mitochondrion	mitochondrion [IDA]			310
Q12658 UniProt NPD GO	IMDH_PNECA	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.11	-	cyt	0					454
Q91UZ5 UniProt NPD GO	IMPA2_MOUSE	Inositol monophosphatase 2 (EC 3.1.3.25) (IMPase 2) (IMP 2) (Inositol-1(or 4)-monophosphatase 2) (My ...	0.11	-	cyt	0					290
Q8CIN7 UniProt NPD GO	IMPA2_RAT	Inositol monophosphatase 2 (EC 3.1.3.25) (IMPase 2) (IMP 2) (Inositol-1(or 4)-monophosphatase 2) (My ...	0.11	-	cyt	0					290
P01331 UniProt NPD GO	INS_PROGU	Insulin [Contains: Insulin B chain; Insulin A chain]	0.11	-	nuc	0	Secreted protein				50
P01329 UniProt NPD GO	INS_CAVPO	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.11	-	vac	0	Secreted protein				110
P06306 UniProt NPD GO	INS_FELCA	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.11	-	exc	0	Secreted protein				110
Q8HXV2 UniProt NPD GO	INS_PONPY	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.11	-	vac	0	Secreted protein				110
P01325 UniProt NPD GO	INS1_MOUSE	Insulin-1 precursor [Contains: Insulin-1 B chain; Insulin-1 A chain]	0.11	-	mit	0	Secreted protein				108
O43736 UniProt NPD GO	ITM2A_HUMAN	Integral membrane protein 2A (E25 protein)	0.11	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)		300222		263
Q86V85 UniProt NPD GO	GP180_HUMAN	Integral membrane protein GPR180 precursor	0.11	-	end	7	Membrane; multi-pass membrane protein (Potential)				440
Q8BPS4 UniProt NPD GO	GP180_MOUSE	Integral membrane protein GPR180 precursor	0.11	-	end	7	Membrane; multi-pass membrane protein (Potential)				441
P39719 UniProt NPD GO	YAF3_YEAST	Integral membrane protein YAL053W	0.11	-	end	9	Membrane; multi-pass membrane protein				783
O88310 UniProt NPD GO	ITL1A_MOUSE	Intelectin-1a precursor (Intestinal lactoferrin receptor) (Galactofuranose-binding lectin)	0.11	-	vac	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein (By similarity)				313
P04365 UniProt NPD GO	IATR_HORSE	Inter-alpha-trypsin inhibitor (ITI) (HI-14) (EI-14) (Inhibitory fragment of ITI) (Fragment)	0.11	-	nuc	0	Secreted protein				125
Q9JL16 UniProt NPD GO	ISG20_MOUSE	Interferon-stimulated gene 20 kDa protein (EC 3.1.13.1) (Promyelocytic leukemia nuclear body-associa ...	0.11	-	cyt	0	Nucleus (By similarity)				300
Q6P8G1 UniProt NPD GO	ILF2_XENTR	Interleukin enhancer-binding factor 2 homolog	0.11	-	mit	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			388
Q866G3 UniProt NPD GO	IL12B_BUBBU	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.11	-	exc	1 *	Secreted protein				327
Q28028 UniProt NPD GO	IL15_BOVIN	Interleukin-15 precursor (IL-15)	0.11	-	mit	0	Secreted protein				162
O97687 UniProt NPD GO	IL15_FELCA	Interleukin-15 precursor (IL-15)	0.11	-	exc	0	Secreted protein				162
Q3Y5G8 UniProt NPD GO	IL15_RABIT	Interleukin-15 precursor (IL-15)	0.11	-	exc	0	Secreted protein				162
Q9XS58 UniProt NPD GO	IL4_TURTR	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.11	-	exc	0	Secreted protein				133
P22273 UniProt NPD GO	IL6RA_RAT	Interleukin-6 receptor alpha chain precursor (IL-6R-alpha) (IL-6R 1) (CD126 antigen)	0.11	-	end	2 *	Membrane; single-pass type I membrane protein				462
P28053 UniProt NPD GO	MMP1_BOVIN	Interstitial collagenase precursor (EC 3.4.24.7) (Matrix metalloproteinase-1) (MMP-1) (Fibroblast co ...	0.11	-	exc	0					469
P40912 UniProt NPD GO	INV1_HANAN	Invertase precursor (EC 3.2.1.26) (Beta-fructofuranosidase 2) (Saccharase)	0.11	-	cyt	0					550
P28297 UniProt NPD GO	ACEA_ARATH	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.11	-	cyt	0	Glyoxysome				576
Q39664 UniProt NPD GO	IDI2_CLAXA	Isopentenyl-diphosphate delta-isomerase II (EC 5.3.3.2) (IPP isomerase II) (Isopentenyl pyrophosphat ...	0.11	-	mit	0					290
P83306 UniProt NPD GO	JAP2_RANJA	Japonicin-2	0.11	-	nuc	0	Secreted protein				21
Q6CIC9 UniProt NPD GO	JHD1_KLULA	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.11	-	cyt	0	Nucleus (By similarity)				478
O88792 UniProt NPD GO	JAM1_MOUSE	Junctional adhesion molecule A precursor (JAM-A) (Junctional adhesion molecule 1) (JAM-1) (CD321 ant ...	0.11	-	nuc	1	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein. Localized at ...	tight junction [IMP]		1F97	300
Q9JHY1 UniProt NPD GO	JAM1_RAT	Junctional adhesion molecule A precursor (JAM-A) (Junctional adhesion molecule 1) (JAM-1) (CD321 ant ...	0.11	-	nuc	1	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein (By similarit ...				300
P15816 UniProt NPD GO	NXLB1_BUNMU	Kappa-2-bungarotoxin precursor (Long neurotoxin CB1) (Kappa neurotoxin)	0.11	-	nuc	0	Secreted protein				87
O12962 UniProt NPD GO	NXL5_BUNMU	Kappa-5-bungarotoxin precursor	0.11	-	nuc	0	Secreted protein				87
P04468 UniProt NPD GO	CASK_RAT	Kappa-casein precursor	0.11	-	mit	0	Secreted protein				178
Q5XIA9 UniProt NPD GO	KLD8B_RAT	Kelch domain-containing protein 8B	0.11	-	cyt	0					354
O95198 UniProt NPD GO	KLHL2_HUMAN	Kelch-like protein 2 (Actin-binding protein Mayven)	0.11	-	cyt	0		actin cytoskeleton [TAS]	605774		593
Q9U6Z1 UniProt NPD GO	KM11_TRYCR	Kinetoplastid membrane protein 11 (KMP-11)	0.11	-	nuc	0	Cytoplasm. Associated with microtubules	microtubule cytoskeleton [IDA]			92
Q99N43 UniProt NPD GO	KREM1_MOUSE	Kremen protein 1 precursor (Kringle-containing protein marking the eye and the nose) (Kringle domain ...	0.11	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			473
P58910 UniProt NPD GO	KURT_PARTR	Kurtoxin (Ktx)	0.11	-	nuc	0	Secreted protein			1T1T	63
Q91WN4 UniProt NPD GO	KMO_MOUSE	Kynurenine 3-monooxygenase (EC 1.14.13.9) (Kynurenine 3-hydroxylase)	0.11	-	end	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			479
Q90YK3 UniProt NPD GO	GGLO_SCYTO	L-gulonolactone oxidase (EC 1.1.3.8) (LGO) (L-gulono-gamma-lactone oxidase) (GLO)	0.11	-	nuc	1	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				440
Q9LDF2 UniProt NPD GO	LAG11_ARATH	LAG1 longevity assurance homolog 1 (LAG1 homolog 1)	0.11	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				310
Q2KIA3 UniProt NPD GO	LMO3_BOVIN	LIM-only protein 3	0.11	-	nuc	0					145
Q5RBW7 UniProt NPD GO	LMO3_PONPY	LIM-only protein 3	0.11	-	nuc	0					145
Q8BZL8 UniProt NPD GO	LMO3_MOUSE	LIM-only protein 3 (Neuronal-specific transcription factor DAT1)	0.11	-	nuc	0					145
Q8TAP4 UniProt NPD GO	LMO3_HUMAN	LIM-only protein 3 (Neuronal-specific transcription factor DAT1) (Rhombotin-3)	0.11	-	nuc	0			180386		145
O49651 UniProt NPD GO	LBD32_ARATH	LOB domain-containing protein 32	0.11	-	nuc	0					192
Q02075 UniProt NPD GO	LAC2_THACU	Laccase 2 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.11	-	exc	0	Secreted protein				599

You are viewing entries 62901 to 62950 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.