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
Q6FWV2 UniProt NPD GO	ATP10_CANGA	Mitochondrial ATPase complex subunit ATP10	0.08	-	mit	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				273
Q505J6 UniProt NPD GO	GHC2_RAT	Mitochondrial glutamate carrier 2 (GC-2) (Glutamate/H(+) symporter 2) (Solute carrier family 25 memb ...	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				315
Q6FRE1 UniProt NPD GO	TIM13_CANGA	Mitochondrial import inner membrane translocase subunit TIM13	0.08	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q4I6B0 UniProt NPD GO	TIM13_GIBZE	Mitochondrial import inner membrane translocase subunit TIM13	0.08	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				82
P32897 UniProt NPD GO	TIM23_YEAST	Mitochondrial import inner membrane translocase subunit TIM23 (Mitochondrial protein import protein ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein. Mitochondrion; mitochondri ...	mitochondrial inner membrane presequence tr... [TAS] mitochondrion [IDA]			222
Q8AVK1 UniProt NPD GO	TI13B_XENLA	Mitochondrial import inner membrane translocase subunit Tim13 B	0.08	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				96
P46757 UniProt NPD GO	RT08_ACACA	Mitochondrial ribosomal protein S8	0.08	-	mit	0	Mitochondrion				127
Q8R0Z5 UniProt NPD GO	MFRN2_MOUSE	Mitoferrin-2 (Mitochondrial iron transporter 2) (Solute carrier family 25 member 28) (Mitochondrial ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein. Isoform 1 and isoform 2 ar ...	mitochondrion [IDA]			364
Q96A46 UniProt NPD GO	MFRN2_HUMAN	Mitoferrin-2 (Mitochondrial iron transporter 2) (Solute carrier family 25 member 28) (Mitochondrial ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein. Isoform 1 and isoform 2 ar ...		609767		364
Q9S7U9 UniProt NPD GO	M2K2_ARATH	Mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (AtMKK2) (AtMAP2Kbeta) ...	0.08	-	cyt	0					363
P40958 UniProt NPD GO	MAD2_YEAST	Mitotic spindle checkpoint component MAD2 (Mitotic MAD2 protein)	0.08	-	mit	0	Nucleus	condensed nuclear chromosome kinetochore [IDA] nuclear pore [IDA]			196
P53987 UniProt NPD GO	MOT1_RAT	Monocarboxylate transporter 1 (MCT 1)	0.08	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)				494
Q02784 UniProt NPD GO	GLRX5_YEAST	Monothiol glutaredoxin-5, mitochondrial precursor	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			150
Q95M54 UniProt NPD GO	OPRM_MACFA	Mu-type opioid receptor (MOR-1)	0.08	-	end	7	Membrane; multi-pass membrane protein				400
Q5IS84 UniProt NPD GO	OPRM_SAIBB	Mu-type opioid receptor (MOR-1)	0.08	-	end	7	Membrane; multi-pass membrane protein (By similarity)				400
Q9W727 UniProt NPD GO	TXML_BUNMU	Muscarinic toxin-like protein precursor	0.08	-	nuc	0	Secreted protein				86
P14318 UniProt NPD GO	MP20_DROME	Muscle-specific protein 20	0.08	-	mit	0					184
Q61096 UniProt NPD GO	PRTN3_MOUSE	Myeloblastin precursor (EC 3.4.21.76) (Proteinase 3) (PR-3)	0.08	-	mit	0					254
P04247 UniProt NPD GO	MYG_MOUSE	Myoglobin	0.08	-	cyt	0					153
P12829 UniProt NPD GO	MYL4_HUMAN	Myosin light polypeptide 4 (Myosin light chain 1, embryonic muscle/atrial isoform) (Myosin light cha ...	0.08	-	cyt	0			160770		196
P04112 UniProt NPD GO	MLRB_PATYE	Myosin regulatory light chain B, smooth adductor muscle	0.08	-	nuc	0					156
P24330 UniProt NPD GO	MYX_CROAD	Myotoxin (CAM-toxin)	0.08	-	nuc	0	Secreted protein				45
Q9SAV1 UniProt NPD GO	MB11_ARATH	Myrosinase-binding protein-like At1g52030 (MBP)	0.08	-	cyt	0					642
Q875I3 UniProt NPD GO	TRPF_HANAN	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.08	-	cyt	0					232
O95671 UniProt NPD GO	ASML_HUMAN	N-acetylserotonin O-methyltransferase-like protein (ASMTL)	0.08	-	cyt	0			400011		621
Q9CPT3 UniProt NPD GO	NANP_MOUSE	N-acylneuraminate-9-phosphatase (EC 3.1.3.29) (Neu5Ac-9-Pase) (Haloacid dehalogenase-like hydrolase ...	0.08	-	cyt	0				2GFH	248
P05982 UniProt NPD GO	NQO1_RAT	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) (Quinone reductase 1) (NAD(P)H:quinone oxidoreductase ...	0.08	-	mit	0	Cytoplasm			1QRD	273
P78736 UniProt NPD GO	XYL1_PACTA	NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.08	-	cyt	0					318
Q68RV6 UniProt NPD GO	NU4C_PANGI	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.08	-	end	14 *	Plastid; chloroplast				500
Q6L3E0 UniProt NPD GO	NU4C_SACHY	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.08	-	end	14 *	Plastid; chloroplast				500
P06262 UniProt NPD GO	NU4C_TOBAC	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.08	-	end	13 *	Plastid; chloroplast				500
O98691 UniProt NPD GO	NUCC_HORVU	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.08	-	cyt	0	Plastid; chloroplast				393
P56754 UniProt NPD GO	NUGC_ARATH	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.08	-	cyt	0	Plastid; chloroplast				158
Q9Y6E7 UniProt NPD GO	SIRT4_HUMAN	NAD-dependent deacetylase sirtuin-4 (EC 3.5.1.-) (SIR2-like protein 4)	0.08	-	mit	0			604482		314
Q95KV7 UniProt NPD GO	NDUAD_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.08	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; matrix side (Probable). May be translocated into the nu ...	cytoplasm [ISS] mitochondrial electron transport chain [IDA] mitochondrion [IDA] nucleoplasm [ISS]			143
Q16718 UniProt NPD GO	NDUA5_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side		601677		115
Q02374 UniProt NPD GO	NDUB2_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial precursor (EC 1.6.5.3) (E ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				108
O95169 UniProt NPD GO	NDUB8_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial precursor (EC 1.6.5.3) (E ...	0.08	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side		602140		186
Q9DCN2 UniProt NPD GO	NCB5R_MOUSE	NADH-cytochrome b5 reductase (EC 1.6.2.2) (B5R) (Diaphorase-1) (Cytochrome b5 reductase 3) [Contains ...	0.08	-	cyt	0	Isoform 1: Endoplasmic reticulum; endoplasmic reticulum membrane; lipid-anchor; cytoplasmic side (By ...	mitochondrial inner membrane [IDA]			300
P19234 UniProt NPD GO	NUHM_RAT	NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3)	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane				248
P49821 UniProt NPD GO	NUBM_HUMAN	NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrial inner membrane [NAS]	256000		464
Q02376 UniProt NPD GO	NIKM_BOVIN	NADH-ubiquinone oxidoreductase KFYI subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Com ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				76
Q37381 UniProt NPD GO	NU1M_ACACA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.08	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				369
P48898 UniProt NPD GO	NU1M_CHOCR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.08	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				326
Q37313 UniProt NPD GO	NU1M_DICDI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.08	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				317
P03886 UniProt NPD GO	NU1M_HUMAN	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.08	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)	respiratory chain complex I (sensu Eukaryota) [NAS]	540000		318
P31839 UniProt NPD GO	NU1M_OENBE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.08	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				331
P34849 UniProt NPD GO	NU2M_APILI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.08	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				333
Q9T9X8 UniProt NPD GO	NU2M_PONPY	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.08	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P03900 UniProt NPD GO	NU3M_XENLA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.08	-	end	3 *					114

You are viewing entries 68451 to 68500 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.