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
P35996 UniProt NPD GO	RM38_YEAST	Mitochondrial 60S ribosomal protein L38 (YmL38) [Contains: Mitochondrial 60S ribosomal protein L34 ( ...	0.03	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			138
Q9GMZ1 UniProt NPD GO	UCP1_CANFA	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				309
Q8K404 UniProt NPD GO	UCP1_DICGR	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				307
Q8N8R3 UniProt NPD GO	MCATL_HUMAN	Mitochondrial carnitine/acylcarnitine carrier protein CACL (CACT-like) (Solute carrier family 25 mem ...	0.03	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				303
Q5R5M0 UniProt NPD GO	MTCH2_PONPY	Mitochondrial carrier homolog 2	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				303
Q9Y6C9 UniProt NPD GO	MTCH2_HUMAN	Mitochondrial carrier homolog 2 (Met-induced mitochondrial protein)	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				303
Q6FPU1 UniProt NPD GO	TIM14_CANGA	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.03	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				153
Q4I7T5 UniProt NPD GO	TIM14_GIBZE	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.03	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				105
Q9LHE5 UniProt NPD GO	TO401_ARATH	Mitochondrial import receptor subunit TOM40 homolog 1 (Translocase of outer membrane 40 kDa subunit ...	0.03	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				308
Q07335 UniProt NPD GO	TOM22_NEUCR	Mitochondrial import receptor subunit tom-22 (Mitochondrial 22 kDa outer membrane protein) (MOM22 pr ...	0.03	-	mit	1	Mitochondrion; mitochondrial outer membrane; single-pass type II membrane protein				154
P08580 UniProt NPD GO	RT16_NEUCR	Mitochondrial ribosomal protein S16 (S24)	0.03	-	mit	0	Mitochondrion				107
Q9GCB9 UniProt NPD GO	RT02_ARATH	Mitochondrial ribosomal protein S2	0.03	-	nuc	0	Mitochondrion				219
P56501 UniProt NPD GO	UCP3_MOUSE	Mitochondrial uncoupling protein 3 (UCP 3)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrion [IMP]			308
O97649 UniProt NPD GO	UCP3_PIG	Mitochondrial uncoupling protein 3 (UCP 3)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				308
P56499 UniProt NPD GO	UCP3_RAT	Mitochondrial uncoupling protein 3 (UCP 3)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrion [TAS]			308
Q620A6 UniProt NPD GO	MFRN_CAEBR	Mitoferrin	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				311
Q3T132 UniProt NPD GO	MAPIP_BOVIN	Mitogen-activated protein-binding protein-interacting protein	0.03	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...				125
Q9Y2Q5 UniProt NPD GO	MAPIP_HUMAN	Mitogen-activated protein-binding protein-interacting protein (Late endosomal/lysosomal Mp1-interact ...	0.03	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...				125
Q9JHS3 UniProt NPD GO	MAPIP_MOUSE	Mitogen-activated protein-binding protein-interacting protein (Late endosomal/lysosomal Mp1-interact ...	0.03	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side. Lys ...			1VEU	125
P87215 UniProt NPD GO	DIMI_SCHPO	Mitosis protein dim1	0.03	-	cyt	0	Nucleus (By similarity)				142
P55846 UniProt NPD GO	MIH_CANPG	Molt-inhibiting hormone (MIH)	0.03	-	cyt	0	Secreted protein				78
Q27225 UniProt NPD GO	MIH_CARMA	Molt-inhibiting hormone precursor (MIH)	0.03	-	mit	1 *	Secreted protein				113
P46882 UniProt NPD GO	AOFN_ASPNG	Monoamine oxidase N (EC 1.4.3.4) (MAO-N)	0.03	-	cyt	0	Peroxisome (Probable)				495
Q15546 UniProt NPD GO	PAQRB_HUMAN	Monocyte to macrophage differentiation protein (Progestin and adipoQ receptor family member XI)	0.03	-	nuc	6 *	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...	integral to plasma membrane [TAS] membrane fraction [TAS]	604467		238
Q9CQY7 UniProt NPD GO	PAQRB_MOUSE	Monocyte to macrophage differentiation protein (Progestin and adipoQ receptor family member XI)	0.03	-	nuc	6 *	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				238
Q719N3 UniProt NPD GO	PAQRB_RAT	Monocyte to macrophage differentiation protein (Progestin and adipoQ receptor family member XI) (Mac ...	0.03	-	nuc	6 *	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein. Lysosome; lysosomal m ...				238
Q43497 UniProt NPD GO	MDAR_LYCES	Monodehydroascorbate reductase (EC 1.6.5.4) (MDAR) (Ascorbate free radical reductase) (AFR reductase ...	0.03	-	cyt	0	Cytoplasm (Probable)				433
P92947 UniProt NPD GO	MDARP_ARATH	Monodehydroascorbate reductase, chloroplast precursor (EC 1.6.5.4) (MDAR)	0.03	-	mit	0	Plastid; chloroplast				493
Q42711 UniProt NPD GO	MDARS_CUCSA	Monodehydroascorbate reductase, seedling isozyme (EC 1.6.5.4) (MDAR seedling) (Ascorbate free radica ...	0.03	-	cyt	0	Cytoplasm (Probable)				434
Q93459 UniProt NPD GO	MRPL_CAEEL	Mrp-family putative nucleotide-binding protein F10G8.6	0.03	-	cyt	0					313
P11062 UniProt NPD GO	TXMG6_AGEAP	Mu-agatoxin-6	0.03	-	nuc	0	Secreted protein				37
O54983 UniProt NPD GO	CRYM_MOUSE	Mu-crystallin homolog	0.03	-	nuc	0	Cytoplasm (By similarity)				313
Q9QYU4 UniProt NPD GO	CRYM_RAT	Mu-crystallin homolog (CDK108)	0.03	-	mit	0	Cytoplasm (By similarity)				313
Q91508 UniProt NPD GO	VSP2_TRIMU	Mucrofibrase-2 precursor (EC 3.4.21.-) (Trimubin)	0.03	-	exc	0	Secreted protein				257
Q8QGR0 UniProt NPD GO	NXM11_DENAN	Muscarinic m1-toxin1 precursor (m1-toxin) (Muscarinic toxin 7) (MT7) (MT-7)	0.03	-	mit	0	Secreted protein	extracellular region [IC]			86
P53777 UniProt NPD GO	MLP1_DROME	Muscle LIM protein 1	0.03	-	nuc	0	Cytoplasm. Nucleus				92
Q10286 UniProt NPD GO	ITR1_SCHPO	Myo-inositol transporter 1	0.03	-	end	12	Membrane; multi-pass membrane protein				575
Q7LZM2 UniProt NPD GO	MYG_ANAPO	Myoglobin	0.03	-	cyt	0					153
P02197 UniProt NPD GO	MYG_CHICK	Myoglobin	0.03	-	cyt	0					153
P02193 UniProt NPD GO	MYG_DIDMA	Myoglobin	0.03	-	mit	0					153
P14397 UniProt NPD GO	MYG_GALGA	Myoglobin	0.03	-	cyt	0					148
P14398 UniProt NPD GO	MYG_GALJA	Myoglobin	0.03	-	cyt	0					148
P02157 UniProt NPD GO	MYG_MELME	Myoglobin	0.03	-	cyt	0					153
P14399 UniProt NPD GO	MYG_MUSAN	Myoglobin	0.03	-	cyt	0					148
P02171 UniProt NPD GO	MYG_OCHPR	Myoglobin	0.03	-	cyt	0					153
P30562 UniProt NPD GO	MYG_PHOSI	Myoglobin	0.03	-	cyt	0					153
P04249 UniProt NPD GO	MYG_PROGU	Myoglobin	0.03	-	cyt	0					153
P02163 UniProt NPD GO	MYG_ROUAE	Myoglobin	0.03	-	cyt	0					153
P04248 UniProt NPD GO	MYG_SPAEH	Myoglobin	0.03	-	cyt	0					153
Q01966 UniProt NPD GO	MYG_SULDI	Myoglobin	0.03	-	cyt	0					377

You are viewing entries 80601 to 80650 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.