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
P52722 UniProt NPD GO	MT1_BRARE	Metallothionein-1 (MT-1)	0.11	-	nuc	0					60
O13269 UniProt NPD GO	MT1_CYPCA	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.11	-	nuc	0					60
P17808 UniProt NPD GO	MT2_MESAU	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.11	-	nuc	0					61
Q8I9B4 UniProt NPD GO	MT4_DROME	Metallothionein-4 (MT-4) (Metallothionein D)	0.11	-	nuc	0					44
O22319 UniProt NPD GO	MT2_MUSAC	Metallothionein-like protein type 2	0.11	-	nuc	0					78
Q42523 UniProt NPD GO	MCCA_ARATH	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4) (3-methylcrotony ...	0.11	-	nuc	0	Mitochondrion; mitochondrial matrix				734
Q96PE7 UniProt NPD GO	MCEE_HUMAN	Methylmalonyl-CoA epimerase, mitochondrial precursor (EC 5.1.99.1) (DL-methylmalonyl-CoA racemase)	0.11	-	mit	0	Mitochondrion (Probable)		608419		176
Q8BMK1 UniProt NPD GO	METL2_MOUSE	Methyltransferase-like protein 2 (EC 2.1.1.-)	0.11	-	nuc	0					389
O75121 UniProt NPD GO	MFA3L_HUMAN	Microfibrillar-associated protein 3-like precursor (Protein kinase NYD-SP9)	0.11	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				409
P82913 UniProt NPD GO	RT15_BOVIN	Mitochondrial 28S ribosomal protein S15 (S15mt) (MRP-S15) (Fragments)	0.11	-	cyt	0	Mitochondrion				96
P82916 UniProt NPD GO	RT17_BOVIN	Mitochondrial 28S ribosomal protein S17 (S17mt) (MRP-S17)	0.11	-	mit	0	Mitochondrion				130
P46768 UniProt NPD GO	RM16_ACACA	Mitochondrial 60S ribosomal protein L16	0.11	-	mit	0	Mitochondrion				141
P34830 UniProt NPD GO	RM16_ACAPO	Mitochondrial 60S ribosomal protein L16 (Fragment)	0.11	-	nuc	0	Mitochondrion				39
Q757F3 UniProt NPD GO	ATP10_ASHGO	Mitochondrial ATPase complex subunit ATP10	0.11	-	mit	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				272
Q32LU1 UniProt NPD GO	MIRO2_BRARE	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (Ras homolog gene family member T2)	0.11	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				617
Q6BHJ3 UniProt NPD GO	TIM10_DEBHA	Mitochondrial import inner membrane translocase subunit TIM10	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				91
Q6CNW2 UniProt NPD GO	TIM14_KLULA	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				163
Q5KQ89 UniProt NPD GO	TIM9_CRYNE	Mitochondrial import inner membrane translocase subunit TIM9	0.11	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
Q6GQ52 UniProt NPD GO	TI10B_XENLA	Mitochondrial import inner membrane translocase subunit Tim10 B	0.11	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
Q66L32 UniProt NPD GO	TIM8A_XENLA	Mitochondrial import inner membrane translocase subunit Tim8 A	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				94
Q9CPQ3 UniProt NPD GO	TOM22_MOUSE	Mitochondrial import receptor subunit TOM22 homolog (Translocase of outer membrane 22 kDa subunit ho ...	0.11	-	cyt	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			141
Q6DEI8 UniProt NPD GO	MIA40_BRARE	Mitochondrial intermembrane space import and assembly protein 40 (Coiled-coil-helix-coiled-coil-heli ...	0.11	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				146
Q9PRP6 UniProt NPD GO	MOTI_CHICK	Motilin	0.11	-	nuc	0	Secreted protein				22
P11057 UniProt NPD GO	TXMG1_AGEAP	Mu-agatoxin-1	0.11	-	nuc	0	Secreted protein			1EIT	36
P00799 UniProt NPD GO	CARP_RHIMI	Mucorpepsin precursor (EC 3.4.23.23) (Mucor rennin)	0.11	-	exc	0				2RMP	430
P81557 UniProt NPD GO	MUEP_SCAVE	Mucus envelope protein (Fragment)	0.11	-	nuc	0	Secreted protein				26
Q06034 UniProt NPD GO	MDR1_LEIEN	Multidrug resistance protein 1 (EC 3.6.3.44) (P-glycoprotein 1)	0.11	-	end	11	Membrane; multi-pass membrane protein				1280
P16875 UniProt NPD GO	MDR1_ENTHI	Multidrug resistance protein 1 (P-glycoprotein) (Fragment)	0.11	-	cyt	0	Membrane; multi-pass membrane protein				114
P16876 UniProt NPD GO	MDR3_ENTHI	Multidrug resistance protein 3 (P-glycoprotein) (Fragment)	0.11	-	cyt	0	Membrane; multi-pass membrane protein				114
Q9M0M2 UniProt NPD GO	MDR9_ARATH	Multidrug resistance protein 9 (P-glycoprotein 9)	0.11	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1323
P60234 UniProt NPD GO	NXM12_DENAN	Muscarinic m1-toxin2	0.11	-	nuc	0	Secreted protein				65
Q5R6H1 UniProt NPD GO	MYADM_PONPY	Myeloid-associated differentiation marker	0.11	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				322
Q96EZ4 UniProt NPD GO	MYEOV_HUMAN	Myeloma overexpressed gene protein (Oncogene in multiple myeloma)	0.11	-	exc	0			605625		313
Q9QZ76 UniProt NPD GO	MYG_RAT	Myoglobin	0.11	-	cyt	0					153
P49824 UniProt NPD GO	MYH7_CANFA	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta) (Fragments)	0.11	-	nuc	0	Thick filaments of the myofibrils				22
P10916 UniProt NPD GO	MLRV_HUMAN	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC-2) (MLC-2v)	0.11	-	cyt	0		cytoskeleton [TAS]	608758		165
P02610 UniProt NPD GO	MLRA_CHICK	Myosin regulatory light chain 2A, cardiac muscle isoform (G2) (MLC-2A)	0.11	-	cyt	0					165
P02611 UniProt NPD GO	MLRB_CHICK	Myosin regulatory light chain 2B, cardiac muscle isoform (G2) (MLC-2B)	0.11	-	cyt	0					163
P08051 UniProt NPD GO	MLR_SPISA	Myosin regulatory light chain, smooth muscle	0.11	-	nuc	0					160
Q39473 UniProt NPD GO	FATB_CINCA	Myristoyl-acyl carrier protein thioesterase, chloroplast precursor (EC 3.1.2.-) (14:0-acyl-carrier p ...	0.11	-	cyt	0	Plastid; chloroplast				382
P29736 UniProt NPD GO	MYRA_SINAL	Myrosinase MA1 (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase)	0.11	-	cyt	0	Vacuole			1W9D	501
P81614 UniProt NPD GO	MYMY_MYTED	Mytimycin (Fragment)	0.11	-	nuc	0	Secreted protein				33
Q9Y2B2 UniProt NPD GO	PIGL_HUMAN	N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase (EC 3.5.1.89) (Phosphatidylinositol-glycan ...	0.11	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)	endoplasmic reticulum [NAS]	605947		252
Q91V57 UniProt NPD GO	CHIN_MOUSE	N-chimaerin (NC) (N-chimerin) (Alpha chimerin) (A-chimaerin) (Rho-GTPase-activating protein 2)	0.11	-	nuc	0					334
Q03503 UniProt NPD GO	MAK3_YEAST	N-terminal acetyltransferase C complex catalytic subunit MAK3 (EC 2.3.1.88) (NatC compolex subunit M ...	0.11	-	cyt	0	Cytoplasm. Nucleus	NatC complex [IDA]			176
Q7F2L3 UniProt NPD GO	NAC48_ORYSA	NAC domain-containing protein 48 (ONAC048)	0.11	-	cyt	0	Nucleus (Probable)				303
P55807 UniProt NPD GO	NRT2_CHICK	NAD(P)(+)--arginine ADP-ribosyltransferase 2 precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)transferase 2 ...	0.11	-	exc	0	Secreted protein; extracellular space. The mature enzyme is probably secreted from granulocytes into ...				312
Q67IL7 UniProt NPD GO	NU2C_ANACO	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IG8 UniProt NPD GO	NU2C_COECR	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IK8 UniProt NPD GO	NU2C_ENSVE	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510

You are viewing entries 63051 to 63100 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.