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
Q9JKW1 UniProt NPD GO	TIM22_RAT	Mitochondrial import inner membrane translocase subunit Tim22	0.01	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				192
Q7T2P6 UniProt NPD GO	TIM23_BRARE	Mitochondrial import inner membrane translocase subunit Tim23	0.01	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...	integral to membrane [TAS] mitochondrial inner membrane presequence tr... [TAS] mitochondrial intermembrane space protein t... [TAS]			208
Q7RX75 UniProt NPD GO	TIM14_NEUCR	Mitochondrial import inner membrane translocase subunit tim-14 (Presequence translocated-associated ...	0.01	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				105
P59670 UniProt NPD GO	TIM17_NEUCR	Mitochondrial import inner membrane translocase subunit tim-17	0.01	-	mit	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				155
Q4WJX5 UniProt NPD GO	TIM10_ASPFU	Mitochondrial import inner membrane translocase subunit tim10	0.01	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
O64497 UniProt NPD GO	TO221_ARATH	Mitochondrial import receptor subunit TOM22 homolog 1 (Translocase of outer membrane 22 kDa subunit ...	0.01	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type II membrane protein (By similarity)				94
Q9XIA7 UniProt NPD GO	TOM6_ARATH	Mitochondrial import receptor subunit TOM6 homolog (Translocase of outer membrane 6 kDa subunit homo ...	0.01	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrion [IDA]			54
Q9ASY8 UniProt NPD GO	TOM7A_ARATH	Mitochondrial import receptor subunit TOM7-1 (Translocase of outer membrane 7 kDa subunit 1)	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				75
Q33569 UniProt NPD GO	RT12_TRYBO	Mitochondrial ribosomal protein S12	0.01	-	end	2 *	Mitochondrion				87
P55916 UniProt NPD GO	UCP3_HUMAN	Mitochondrial uncoupling protein 3 (UCP 3)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [TAS] mitochondrion [TAS]	602044		312
Q6DEG4 UniProt NPD GO	MAPIP_BRARE	Mitogen-activated protein-binding protein-interacting protein	0.01	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...				125
Q9N2U6 UniProt NPD GO	MAPIP_CAEEL	Mitogen-activated protein-binding protein-interacting protein homolog	0.01	-	cyt	0					124
Q9LU93 UniProt NPD GO	MAD2_ARATH	Mitotic spindle checkpoint protein MAD2	0.01	-	cyt	0	Nucleus (Probable)				209
P18998 UniProt NPD GO	PA2A_CROSS	Mojave toxin acidic chain precursor (Mtx-a) [Contains: Mojave toxin acidic chain A; Mojave toxin aci ...	0.01	-	exc	0	Secreted protein				138
Q10987 UniProt NPD GO	MIH_PROBO	Molt-inhibiting hormone precursor (MIH) (Fragment)	0.01	-	cyt	0	Secreted protein				74
O96033 UniProt NPD GO	MOS2S_HUMAN	Molybdenum cofactor synthesis protein 2 small subunit (Molybdopterin-synthase small subunit) (MOCS2A ...	0.01	-	cyt	0		molybdopterin synthase complex [NAS]	603708		88
P02882 UniProt NPD GO	MONB_DIOCU	Monellin chain B (Monellin chain II)	0.01	-	cyt	0				4MON	50
Q8R431 UniProt NPD GO	MGLL_RAT	Monoglyceride lipase (EC 3.1.1.23) (MGL)	0.01	-	mit	0					303
Q8VI63 UniProt NPD GO	MOB2_MOUSE	Mps one binder kinase activator-like 2 (Mob2 homolog) (Ovary-specific MOB-like protein)	0.01	-	cyt	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity)				235
Q26443 UniProt NPD GO	CXMB_CONMR	Mu-O-conotoxin MrVIB precursor	0.01	-	exc	2 *	Secreted protein			1RMK	82
P58926 UniProt NPD GO	CXM4A_CONPE	Mu-conotoxin PnIVA	0.01	-		0	Secreted protein				17
P58927 UniProt NPD GO	CXM4B_CONPE	Mu-conotoxin PnIVB	0.01	-		0	Secreted protein				17
P97266 UniProt NPD GO	OPRM_CAVPO	Mu-type opioid receptor (MOR-1) (Fragment)	0.01	-	vac	2 *	Membrane; multi-pass membrane protein				98
Q07938 UniProt NPD GO	MEU1_YEAST	Multicopy enhancer of UAS2	0.01	-	mit	0		cytoplasm [IDA]			337
Q8K5B2 UniProt NPD GO	MCFD2_MOUSE	Multiple coagulation factor deficiency protein 2 homolog precursor (Neural stem cell-derived neurona ...	0.01	-	exc	0	Endoplasmic reticulum-Golgi intermediate compartment (By similarity)				145
Q8K5B3 UniProt NPD GO	MCFD2_RAT	Multiple coagulation factor deficiency protein 2 homolog precursor (Neural stem cell-derived neurona ...	0.01	-	exc	0	Endoplasmic reticulum-Golgi intermediate compartment (By similarity)	extracellular region [IDA]			145
Q3ZBY0 UniProt NPD GO	MAL_BOVIN	Myelin and lymphocyte protein	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				153
Q28296 UniProt NPD GO	MAL_CANFA	Myelin and lymphocyte protein (T-lymphocyte maturation-associated protein) (VIP17 proteolipid)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				153
P23289 UniProt NPD GO	MYPR_CHICK	Myelin proteolipid protein (PLP) (Lipophilin)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				276
P79826 UniProt NPD GO	MYPR_ONCMY	Myelin proteolipid protein (PLP) (Lipophilin) (DM20)	0.01	-	end	3 *	Membrane; multi-pass membrane protein				258
P02151 UniProt NPD GO	MYG_AOTTR	Myoglobin	0.01	-	cyt	0					153
P02152 UniProt NPD GO	MYG_CALJA	Myoglobin	0.01	-	cyt	0					153
P56208 UniProt NPD GO	MYG_CARCR	Myoglobin	0.01	-	cyt	0				1LHT	153
P14396 UniProt NPD GO	MYG_CASFI	Myoglobin	0.01	-	cyt	0					153
P02153 UniProt NPD GO	MYG_CEBAP	Myoglobin	0.01	-	cyt	0					153
P02202 UniProt NPD GO	MYG_CHEMY	Myoglobin	0.01	-	cyt	0					153
P02204 UniProt NPD GO	MYG_CYPCA	Myoglobin	0.01	-	cyt	0					146
P83682 UniProt NPD GO	MYG_DELLE	Myoglobin	0.01	-	cyt	0					153
P02186 UniProt NPD GO	MYG_ELEMA	Myoglobin	0.01	-	cyt	0				1EMY	153
P68083 UniProt NPD GO	MYG_EQUBU	Myoglobin	0.01	-	cyt	0					153
P68086 UniProt NPD GO	MYG_ERYPA	Myoglobin	0.01	-	cyt	0					153
P02177 UniProt NPD GO	MYG_ESCGI	Myoglobin	0.01	-	cyt	0					153
P02168 UniProt NPD GO	MYG_GALCR	Myoglobin	0.01	-	cyt	0					153
P02147 UniProt NPD GO	MYG_GORBE	Myoglobin	0.01	-	cyt	0					153
P68082 UniProt NPD GO	MYG_HORSE	Myoglobin	0.01	-	cyt	0				1YMC	153
P02144 UniProt NPD GO	MYG_HUMAN	Myoglobin	0.01	-	cyt	0			160000	2MM1	153
P62734 UniProt NPD GO	MYG_HYLAG	Myoglobin	0.01	-	cyt	0					153
P62735 UniProt NPD GO	MYG_HYLSY	Myoglobin	0.01	-	cyt	0					153
P02154 UniProt NPD GO	MYG_LAGLA	Myoglobin	0.01	-	cyt	0					153
P02169 UniProt NPD GO	MYG_LEPMU	Myoglobin	0.01	-	cyt	0					153

You are viewing entries 89601 to 89650 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.