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
Q9DC70 UniProt NPD GO	NUKM_MOUSE	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.17	-	mit	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			224
Q22619 UniProt NPD GO	NUIM_CAEEL	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.17	-	mit	0					212
Q9ZXY4 UniProt NPD GO	NU1M_PAPHA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.17	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q8W9N5 UniProt NPD GO	NU2M_DUGDU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.17	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q85PP8 UniProt NPD GO	NU2M_GENSE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.17	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q85PS1 UniProt NPD GO	NU2M_MUNMN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.17	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q35535 UniProt NPD GO	NU2M_PETMA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.17	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P11992 UniProt NPD GO	NU4M_ASTPE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.17	-	end	13 *					460
Q36423 UniProt NPD GO	NU4LM_LOCMI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.17	-	end	3 *					97
P92485 UniProt NPD GO	NU5M_EQUAS	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.17	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
P48656 UniProt NPD GO	NU5M_HORSE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.17	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				604
P00389 UniProt NPD GO	NCPR_RABIT	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.17	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				679
P00388 UniProt NPD GO	NCPR_RAT	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.17	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...			1JA1	677
Q99406 UniProt NPD GO	TYBN_HUMAN	NB thymosin beta (Thymosin-like protein 8)	0.17	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [NAS]			44
Q9VTE9 UniProt NPD GO	ULA1_DROME	NEDD8-activating enzyme E1 regulatory subunit	0.17	-	nuc	0		insoluble fraction [ISS]			524
Q5ZIE6 UniProt NPD GO	ULA1_CHICK	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (APP-BP1)	0.17	-	nuc	0					535
Q91044 UniProt NPD GO	NTRK3_CHICK	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3) ( ...	0.17	-	nuc	2 *	Membrane; single-pass type I membrane protein				827
Q28142 UniProt NPD GO	NRX1B_BOVIN	Neurexin-1-beta precursor (Neurexin I-beta)	0.17	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				467
P58400 UniProt NPD GO	NRX1B_HUMAN	Neurexin-1-beta precursor (Neurexin I-beta)	0.17	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		600565		442
Q8WMI6 UniProt NPD GO	NXPH1_MACMU	Neurexophilin-1 (Fragment)	0.17	-	nuc	0	Secreted protein (Potential)				104
Q9Z2N4 UniProt NPD GO	NXPH4_RAT	Neurexophilin-4 precursor	0.17	-	mit	0	Secreted protein (Potential)				304
Q9ER97 UniProt NPD GO	NGB_MOUSE	Neuroglobin	0.17	-	cyt	0				1W92	151
Q99JA8 UniProt NPD GO	NGB_RAT	Neuroglobin	0.17	-	cyt	0					151
P43144 UniProt NPD GO	ACHA9_RAT	Neuronal acetylcholine receptor protein subunit alpha-9 precursor (Nicotinic acetylcholine receptor ...	0.17	-	end	4	Membrane; multi-pass membrane protein (Probable)	nicotinic acetylcholine-gated receptor-chan... [IDA]			479
Q9EP86 UniProt NPD GO	NPFF1_RAT	Neuropeptide FF receptor 1 (G-protein coupled receptor 147) (RFamide-related peptide receptor OT7T02 ...	0.17	-	end	7 *	Membrane; multi-pass membrane protein				432
Q9PTA0 UniProt NPD GO	NEUY_DICLA	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.17	-	exc	1 *	Secreted protein				99
O95665 UniProt NPD GO	NTR2_HUMAN	Neurotensin receptor type 2 (NT-R-2) (Levocabastine-sensitive neurotensin receptor) (NTR2 receptor)	0.17	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	605538		410
Q304B9 UniProt NPD GO	NCASE_ARATH	Neutral ceramidase precursor (EC 3.5.1.23) (NCDase) (N-CDase) (Acylsphingosine deacylase) (N-acylsph ...	0.17	-	end	1 *	Secreted protein (Potential)				757
P07467 UniProt NPD GO	DEF5_RABIT	Neutrophil antibiotic peptide NP-4 precursor (Microbicidal peptide NP-4)	0.17	-	exc	0	Secreted protein				95
Q99JR6 UniProt NPD GO	NMNA3_MOUSE	Nicotinamide mononucleotide adenylyltransferase 3 (EC 2.7.7.1) (NMN adenylyltransferase 3)	0.17	-	mit	0	Nucleus (Probable)				245
P27968 UniProt NPD GO	NIA7_HORVU	Nitrate reductase [NAD(P)H] (EC 1.7.1.2)	0.17	-	cyt	0					891
P23312 UniProt NPD GO	NIA_SPIOL	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.17	-	nuc	0					926
P08619 UniProt NPD GO	NIA_NEUCR	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.17	-	cyt	0					982
Q42965 UniProt NPD GO	NRL4_TOBAC	Nitrilase 4 (EC 3.5.5.1)	0.17	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Tightly associated with the plasma mem ...				349
Q15155 UniProt NPD GO	NOMO1_HUMAN	Nodal modulator 1 precursor (pM5)	0.17	-	end	0	Membrane; single-pass type I membrane protein (Probable)		609157		1222
P69849 UniProt NPD GO	NOMO3_HUMAN	Nodal modulator 3 precursor (pM5 protein 3)	0.17	-	end	0	Membrane; single-pass type I membrane protein (Potential)		609159		1222
Q8SPY7 UniProt NPD GO	RNAS2_PAPHA	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.17	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule (By similarity)				160
O04004 UniProt NPD GO	NLTP6_AMBAR	Nonspecific lipid-transfer protein precursor (LTP) (Pollen allergen Amb a 6) (Amb a VI) (Allergen Ra ...	0.17	-	mit	0					118
Q3ZBJ1 UniProt NPD GO	NCBP2_BOVIN	Nuclear cap-binding protein subunit 2	0.17	-	nuc	0	Nucleus (By similarity)				156
Q9CQ49 UniProt NPD GO	NCBP2_MOUSE	Nuclear cap-binding protein subunit 2 (20 kDa nuclear cap-binding protein) (NCBP 20 kDa subunit) (CB ...	0.17	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			156
P52298 UniProt NPD GO	NCBP2_HUMAN	Nuclear cap-binding protein subunit 2 (20 kDa nuclear cap-binding protein) (NCBP 20 kDa subunit) (CB ...	0.17	-	nuc	0	Nucleus	nucleus [IDA]	605133	1N54	156
Q32KP9 UniProt NPD GO	NTF2_BOVIN	Nuclear transport factor 2 (NTF-2)	0.17	-	cyt	0	Cytoplasm (By similarity)				127
P61971 UniProt NPD GO	NTF2_MOUSE	Nuclear transport factor 2 (NTF-2)	0.17	-	cyt	0	Cytoplasm (By similarity)				127
P61972 UniProt NPD GO	NTF2_RAT	Nuclear transport factor 2 (NTF-2)	0.17	-	cyt	0	Cytoplasm (By similarity)			1U5O	127
P61970 UniProt NPD GO	NTF2_HUMAN	Nuclear transport factor 2 (NTF-2) (Placental protein 15) (PP15)	0.17	-	cyt	0	Cytoplasm		605813	1GY5	127
O42242 UniProt NPD GO	NTF2_XENLA	Nuclear transport factor 2 (NTF-2) (p10)	0.17	-	cyt	0	Cytoplasm (By similarity)				127
P81919 UniProt NPD GO	OR46A_DROME	Odorant receptor 46a, isoform A	0.17	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			381
Q9TU86 UniProt NPD GO	OR1G1_GORGO	Olfactory receptor 1G1	0.17	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NGH8 UniProt NPD GO	O56A4_HUMAN	Olfactory receptor 56A4	0.17	-	end	6 *	Membrane; multi-pass membrane protein				313
Q13606 UniProt NPD GO	OR5I1_HUMAN	Olfactory receptor 5I1 (Olfactory receptor-like protein OLF1) (Olfactory receptor OR11-159)	0.17	-	end	7 *	Membrane; multi-pass membrane protein		608496		314

You are viewing entries 54601 to 54650 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.