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
Q99KK2 UniProt NPD GO	NEUA_MOUSE	N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) (CMP-N-acetylneuraminic acid synthetase) (CMP-N ...	0.12	-	mit	0	Nucleus			1QWJ	432
P36416 UniProt NPD GO	ARD1H_DICDI	N-terminal acetyltransferase complex ARD1 subunit homolog (EC 2.3.1.-)	0.12	-	mit	0					203
Q4VZK8 UniProt NPD GO	NU2C_CUCSA	NAD(P)H-quinone oxidoreductase chain 2 (EC 1.6.5.-) (NAD(P)H dehydrogenase I, chain 2) (NDH-1, chain ...	0.12	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q9T3G4 UniProt NPD GO	NU2C_ARATH	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.12	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				512
Q7Y736 UniProt NPD GO	NU2C_CALFE	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.12	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q9MUQ6 UniProt NPD GO	NU2C_MESVI	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.12	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				502
Q589A5 UniProt NPD GO	NU2C_SILLA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.12	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q8M9U1 UniProt NPD GO	NU4C_CHAGL	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.12	-	end	14 *	Plastid; chloroplast				506
Q6ENA7 UniProt NPD GO	NU4C_ORYNI	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.12	-	end	14 *	Plastid; chloroplast				500
P12127 UniProt NPD GO	NU4C_ORYSA	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.12	-	end	14 *	Plastid; chloroplast				500
P92230 UniProt NPD GO	NU5C_AVEFA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.12	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				212
Q6ENH1 UniProt NPD GO	NUGC_ORYNI	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.12	-	cyt	0	Plastid; chloroplast				159
P12200 UniProt NPD GO	NUGC_ORYSA	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.12	-	cyt	0	Plastid; chloroplast				159
Q9NXA8 UniProt NPD GO	SIRT5_HUMAN	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-) (SIR2-like protein 5)	0.12	-	mit	0			604483	2FZQ	310
O95299 UniProt NPD GO	NDUAA_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial precursor (EC 1.6.5.3) ...	0.12	-	mit	0	Mitochondrion; mitochondrial matrix		603835		355
Q4R6H1 UniProt NPD GO	NDUAD_MACFA	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.12	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein; matrix side (By similarit ...				163
P23935 UniProt NPD GO	NDUA5_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.12	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				115
P20070 UniProt NPD GO	NCB5R_RAT	NADH-cytochrome b5 reductase (EC 1.6.2.2) (B5R) (Diaphorase-1) (Cytochrome b5 reductase 3) [Contains ...	0.12	-	mit	0	Isoform 1: Endoplasmic reticulum; endoplasmic reticulum membrane; lipid-anchor; cytoplasmic side. Mi ...	soluble fraction [TAS]		1QX4	300
P42116 UniProt NPD GO	NURM_NEUCR	NADH-ubiquinone oxidoreductase 17.8 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				186
Q9TC96 UniProt NPD GO	NUCM_NEPOL	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.12	-	cyt	0	Mitochondrion				398
Q92406 UniProt NPD GO	NUBM_ASPNG	NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				496
O43677 UniProt NPD GO	NIKM_HUMAN	NADH-ubiquinone oxidoreductase KFYI subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Com ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side		603844		76
O99824 UniProt NPD GO	NU1M_RHISA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.12	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				313
O21408 UniProt NPD GO	NU1M_SCYCA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.12	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
P03890 UniProt NPD GO	NU1M_XENLA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.12	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				323
Q534B1 UniProt NPD GO	NU2M_AILME	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.12	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TGY6 UniProt NPD GO	NU2M_CANRF	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.12	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O78680 UniProt NPD GO	NU2M_CARAU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.12	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
P92660 UniProt NPD GO	NU2M_MACRO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.12	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q2TGY5 UniProt NPD GO	NU2M_POTFL	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.12	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q36458 UniProt NPD GO	NU4M_ORNAN	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.12	-	end	14 *					460
Q95917 UniProt NPD GO	NU4M_POLOR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.12	-	end	12 *					459
P92494 UniProt NPD GO	NU4M_AZEFE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.12	-	end	6 *					231
P50664 UniProt NPD GO	NU4M_MACFA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.12	-	mit	4 *					152
P60498 UniProt NPD GO	NU6M_BRACM	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.12	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				205
Q04894 UniProt NPD GO	ADH6_YEAST	NADP-dependent alcohol dehydrogenase 6 (EC 1.1.1.2) (NADP-dependent alcohol dehydrogenase VI) (ScADH ...	0.12	-	cyt	0		soluble fraction [IDA]		1Q1N	360
P37223 UniProt NPD GO	MAOX_MESCR	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME)	0.12	-	nuc	0	Cytoplasm				585
P61282 UniProt NPD GO	NEDD8_BOVIN	NEDD8 precursor (Ubiquitin-like protein Nedd8) (Neddylin)	0.12	-	cyt	0	Nucleus. Mainly (By similarity)				81
Q15843 UniProt NPD GO	NEDD8_HUMAN	NEDD8 precursor (Ubiquitin-like protein Nedd8) (Neddylin)	0.12	-	cyt	0	Nucleus. Mainly	nucleus [TAS]	603171	2BKR	81
Q4PLJ0 UniProt NPD GO	NEDD8_RABIT	NEDD8 precursor (Ubiquitin-like protein Nedd8) (Neddylin)	0.12	-	cyt	0	Nucleus. Mainly (By similarity)				81
O74549 UniProt NPD GO	UBC12_SCHPO	NEDD8-conjugating enzyme ubc12 (EC 6.3.2.-) (RUB1-conjugating enzyme) (RUB1-protein ligase) (Ubiquit ...	0.12	-	nuc	0					177
Q15653 UniProt NPD GO	IKBB_HUMAN	NF-kappa-B inhibitor beta (NF-kappa-BIB) (I-kappa-B-beta) (IkappaBbeta) (IKB-beta) (IKB-B) (Thyroid ...	0.12	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		604495		356
Q9U757 UniProt NPD GO	NXT1_CAEEL	NTF2-related export protein	0.12	-	nuc	0	Nucleus (By similarity)				137
Q9TM10 UniProt NPD GO	MENB_CYACA	Naphthoate synthase (EC 4.1.3.36) (Dihydroxynaphthoic acid synthetase) (DHNA synthetase)	0.12	-	cyt	0	Plastid; chloroplast				268
Q9LHG9 UniProt NPD GO	NACA1_ARATH	Nascent polypeptide-associated complex subunit alpha-like protein 1 (NAC-alpha-like protein 1) (Alph ...	0.12	-	nuc	0					203
Q8LGC6 UniProt NPD GO	NACA5_ARATH	Nascent polypeptide-associated complex subunit alpha-like protein 5 (NAC-alpha-like protein 5) (Alph ...	0.12	-	cyt	0					209
Q6EV97 UniProt NPD GO	NGB_RABIT	Neuroglobin	0.12	-	cyt	0					151
P34964 UniProt NPD GO	NEUU_PIG	Neuromedin U-25 (NmU-25) [Contains: Neuromedin U-8 (NmU-8)]	0.12	-	cyt	0	Secreted protein				25
O54799 UniProt NPD GO	NMBR_MOUSE	Neuromedin-B receptor (NMB-R) (Neuromedin-B-preferring bombesin receptor)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				390
Q9Y328 UniProt NPD GO	NSG2_HUMAN	Neuron-specific protein family member 2 (Protein p19) (HMP19)	0.12	-	mit	1	Intracytoplasmic membrane; single-pass type II membrane protein (By similarity). Mainly Golgi stack, ...				171

You are viewing entries 61501 to 61550 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.