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
Q9PSJ0 UniProt NPD GO	MYCN_BRARE	N-myc protein (zN-Myc) (Fragment)	0.04	-	cyt	0	Nucleus	nucleus [NAS]			93
Q08689 UniProt NPD GO	NAT5_YEAST	N-terminal acetyltransferase A complex subunit NAT5 (EC 2.3.1.-) (NatA complex subunit NAT5)	0.04	-	mit	0	Cytoplasm	NatA complex [IDA]			176
Q06504 UniProt NPD GO	NAT3_YEAST	N-terminal acetyltransferase B complex catalytic subunit NAT3 (EC 2.3.1.88) (NatB complex subunit NA ...	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA] NatB complex [TAS]			195
P49378 UniProt NPD GO	XYL1_KLULA	NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.04	-	cyt	0					329
Q32RP6 UniProt NPD GO	NU2C_ZYGCR	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.04	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				497
Q9BBP2 UniProt NPD GO	NU4LC_LOTJA	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.04	-	end	3 *	Plastid; chloroplast				101
P06261 UniProt NPD GO	NU4LC_TOBAC	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.04	-	end	3 *	Plastid; chloroplast				101
Q70XV9 UniProt NPD GO	NU1C_AMBTC	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q37165 UniProt NPD GO	NU1C_ARATH	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				360
Q9MTH7 UniProt NPD GO	NU1C_OENHO	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.04	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q2PMN7 UniProt NPD GO	NU1C_SOYBN	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
O35683 UniProt NPD GO	NDUA1_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.04	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrion [IDA]			70
P34942 UniProt NPD GO	NDUAA_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial precursor (EC 1.6.5.3) ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				343
Q9D8B4 UniProt NPD GO	NDUAB_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...	mitochondrion [IDA]			141
Q16795 UniProt NPD GO	NDUA9_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial precursor (EC 1.6.5.3) ( ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	603834		377
Q02378 UniProt NPD GO	NDUB1_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.04	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				57
O75438 UniProt NPD GO	NDUB1_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side		603837		58
Q5R4A8 UniProt NPD GO	NDUB8_PONPY	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial precursor (EC 1.6.5.3) (E ...	0.04	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				186
P80731 UniProt NPD GO	NUO8_SOLTU	NADH-ubiquinone oxidoreductase 12 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-12KD) (CI-12KD) ...	0.04	-		0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				15
P23934 UniProt NPD GO	NUMM_BOVIN	NADH-ubiquinone oxidoreductase 13 kDa-A subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				124
Q20719 UniProt NPD GO	NUHM_CAEEL	NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3)	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				239
Q91YT0 UniProt NPD GO	NUBM_MOUSE	NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			464
P42117 UniProt NPD GO	NDUA3_NEUCR	NADH-ubiquinone oxidoreductase 9.5 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-9.5KD) (CI-9.5) ...	0.04	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				81
P24967 UniProt NPD GO	NU1M_BALPH	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q70Y30 UniProt NPD GO	NU1M_CHODI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P41304 UniProt NPD GO	NU1M_DIDMA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P92475 UniProt NPD GO	NU1M_EQUAS	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q9ZZZ1 UniProt NPD GO	NU1M_HIPAM	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O03847 UniProt NPD GO	NU1M_LATCH	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				323
Q8M891 UniProt NPD GO	NU1M_LONTH	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P08774 UniProt NPD GO	NU1M_NEUCR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				371
Q8M881 UniProt NPD GO	NU1M_NYCVE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q8M892 UniProt NPD GO	NU1M_PHYEO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P19041 UniProt NPD GO	NU1M_PODAN	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				367
O78712 UniProt NPD GO	NU1M_SMIMA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O21397 UniProt NPD GO	NU1M_STRCA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
O78698 UniProt NPD GO	NU1M_TAMSI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q9ZZ38 UniProt NPD GO	NU1M_TRIRU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				343
O80003 UniProt NPD GO	NU1M_NYCNO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragment)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				301
Q8HEC1 UniProt NPD GO	NU2M_CAEBR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				282
P24889 UniProt NPD GO	NU2M_CAEEL	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.04	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				282
P34850 UniProt NPD GO	NU3M_ANOGA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					117
Q2I3G7 UniProt NPD GO	NU3M_ELEMA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					115
Q9T9Y5 UniProt NPD GO	NU3M_GORGO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					115
O03171 UniProt NPD GO	NU3M_LATCH	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					116
O47476 UniProt NPD GO	NU3M_LOLBL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					117
P20687 UniProt NPD GO	NU3M_ONCKI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					116
Q9ZXX7 UniProt NPD GO	NU3M_PAPHA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					115
P48913 UniProt NPD GO	NU3M_PICCA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					148
Q9T9X5 UniProt NPD GO	NU3M_PONPY	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					115

You are viewing entries 77601 to 77650 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.