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
Q7ZV60 UniProt NPD GO	BCS1_BRARE	Mitochondrial chaperone BCS1 (BCS1-like protein)	0.32	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				420
Q6CLP4 UniProt NPD GO	TIM54_KLULA	Mitochondrial import inner membrane translocase subunit TIM54	0.32	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				471
Q6C7Y5 UniProt NPD GO	TIM54_YARLI	Mitochondrial import inner membrane translocase subunit TIM54	0.32	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				572
Q9Y5J6 UniProt NPD GO	TIM9B_HUMAN	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b) (Fracture callus p ...	0.32	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein		607388		103
Q9C1W5 UniProt NPD GO	TIM16_SCHPO	Mitochondrial import inner membrane translocase subunit tim16 (Presequence translocated-associated m ...	0.32	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				128
Q4WIQ2 UniProt NPD GO	TIM9_ASPFU	Mitochondrial import inner membrane translocase subunit tim9	0.32	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
P92792 UniProt NPD GO	TOM20_SOLTU	Mitochondrial import receptor subunit TOM20 (Translocase of outer membrane 20 kDa subunit)	0.32	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				204
P26870 UniProt NPD GO	RT11_MARPO	Mitochondrial ribosomal protein S11	0.32	-	nuc	0	Mitochondrion				125
Q75G41 UniProt NPD GO	RMAR_ASHGO	Mitochondrial ribosomal protein VAR1	0.32	-	nuc	0	Mitochondrion				339
Q95NE7 UniProt NPD GO	MK14_PANTR	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 alpha) (MAP ...	0.32	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			359
Q9DGE2 UniProt NPD GO	MK14A_BRARE	Mitogen-activated protein kinase 14a (EC 2.7.11.24) (Mitogen-activated protein kinase p38a) (MAP kin ...	0.32	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			361
Q8VHN7 UniProt NPD GO	MASS1_MOUSE	Monogenic audiogenic seizure susceptibility protein 1 precursor (Very large G-protein coupled recept ...	0.32	-	end	8 *	Cell membrane; multi-pass membrane protein. Isoforms 4, isoform 5: Secreted protein	membrane [NAS]			6298
O15105 UniProt NPD GO	SMAD7_HUMAN	Mothers against decapentaplegic homolog 7 (SMAD 7) (Mothers against DPP homolog 7) (Smad7) (hSMAD7)	0.32	-	nuc	0	Nucleus. Interaction with NEDD4L induces translocation from the nucleus to the cytoplasm (By similar ...		602932	2DJY	426
Q8VE04 UniProt NPD GO	MOL2B_MOUSE	Mps one binder kinase activator-like 2B (Mob1 homolog 2b)	0.32	-	nuc	0					216
Q62635 UniProt NPD GO	MUC2_RAT	Mucin-2 precursor (Intestinal mucin-2) (Fragment)	0.32	-	exc	0	Secreted protein				1513
P27106 UniProt NPD GO	MIS_MOUSE	Muellerian-inhibiting factor precursor (MIS) (Anti-Muellerian hormone) (AMH) (Muellerian-inhibiting ...	0.32	-	exc	0	Secreted protein (By similarity)	cytoplasm [IDA]			555
P60237 UniProt NPD GO	NXM2_DENAN	Muscarinic m2-toxin (gm60)	0.32	-	mit	0	Secreted protein				63
P56671 UniProt NPD GO	MAZ_MOUSE	Myc-associated zinc finger protein (MAZI) (Purine-binding transcription factor) (Pur-1)	0.32	-	nuc	0	Nucleus (By similarity)				477
P07313 UniProt NPD GO	MYLK2_RABIT	Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.11.18) (MLCK2)	0.32	-	nuc	0	Cytoplasm. Colocalizes with phosphorylated myosin light chain (RLCP) at filaments of the myofibrils			2BBN	607
P13833 UniProt NPD GO	MLR_DICDI	Myosin regulatory light chain (RMLC)	0.32	-	cyt	0					161
P19105 UniProt NPD GO	MLRM_HUMAN	Myosin regulatory light chain 2, nonsarcomeric (Myosin RLC)	0.32	-	mit	0			609211		170
Q5RC34 UniProt NPD GO	MLRM_PONPY	Myosin regulatory light chain 2, nonsarcomeric (Myosin RLC)	0.32	-	mit	0					170
P51688 UniProt NPD GO	SPHM_HUMAN	N-sulphoglucosamine sulphohydrolase precursor (EC 3.10.1.1) (Sulfoglucosamine sulfamidase) (Sulphami ...	0.32	-	exc	0	Lysosome		605270		502
Q02197 UniProt NPD GO	MAK10_YEAST	N-terminal acetyltransferase C complex subunit MAK10 (NatC compolex subunit MAK10) (L-A virus GAG pr ...	0.32	-	cyt	0	Cytoplasm	cytoplasm [IDA] NatC complex [IDA]			733
Q7EZT1 UniProt NPD GO	NAC67_ORYSA	NAC domain-containing protein 67 (ONAC067)	0.32	-	mit	0	Nucleus (Probable)				276
P06410 UniProt NPD GO	NUKC_MARPO	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.32	-	nuc	0	Plastid; chloroplast				243
Q9TKY0 UniProt NPD GO	NUKC_NEPOL	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.32	-	nuc	0	Plastid; chloroplast				237
O98679 UniProt NPD GO	NUKC_PEA	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.32	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane	thylakoid membrane (sensu Viridiplantae) [IDA]			227
Q68RV2 UniProt NPD GO	NUIC_PANGI	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.32	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q3UIU2 UniProt NPD GO	NDUB6_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.32	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrion [IDA]			127
P42028 UniProt NPD GO	NUIM_BOVIN	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.32	-	mit	0					212
Q37373 UniProt NPD GO	NUAM_ACACA	NADH-ubiquinone oxidoreductase 75 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-75KD) (CI-75KD) ...	0.32	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				675
Q9ZZ58 UniProt NPD GO	NU4M_CANFA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.32	-	end	12 *					459
Q598S9 UniProt NPD GO	NU4M_CAPMR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.32	-	end	13 *					459
Q9NPH5 UniProt NPD GO	NOX4_HUMAN	NADPH oxidase 4 (EC 1.6.3.-) (Kidney superoxide-producing NADPH oxidase) (KOX-1) (Renal NAD(P)H-oxid ...	0.32	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cell membrane; m ...	integral to membrane [TAS]	605261		578
Q8TBC4 UniProt NPD GO	UBA3_HUMAN	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3) (NEDD8-act ...	0.32	+	cyt	0			603172	1YOV	463
Q6BRY2 UniProt NPD GO	PHO85_DEBHA	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85)	0.32	-	cyt	0					330
Q8K1S3 UniProt NPD GO	UNC5B_MOUSE	Netrin receptor UNC5B precursor (Unc-5 homolog B) (Unc-5 homolog 2)	0.32	-	end	1	Membrane; single-pass type I membrane protein (By similarity)			1WMG	945
Q9R1A3 UniProt NPD GO	NET2_MOUSE	Netrin-2-like protein precursor (Netrin-3)	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular region [IDA] Golgi apparatus [IDA]			580
Q923S6 UniProt NPD GO	NEURL_MOUSE	Neuralized-like protein 1 (m-neuralized 1) (m-neu1)	0.32	-	mit	0	Cytoplasm; perinuclear region (By similarity)	cytoplasm [IDA] plasma membrane [IDA]			574
Q91VX5 UniProt NPD GO	NXPH3_MOUSE	Neurexophilin-3 precursor	0.32	-	mit	0	Secreted protein (Potential)				252
P19370 UniProt NPD GO	ACHB2_CARAU	Neuronal acetylcholine receptor protein subunit beta-2 (GF-beta-2) (Fragment)	0.32	-	end	4	Membrane; multi-pass membrane protein				459
Q8SPU6 UniProt NPD GO	ACHB4_BOVIN	Neuronal acetylcholine receptor protein subunit beta-4 precursor	0.32	-	end	4	Membrane; multi-pass membrane protein (By similarity)				496
P26153 UniProt NPD GO	ACHB4_CHICK	Neuronal acetylcholine receptor protein subunit beta-4 precursor (Neuronal acetylcholine receptor no ...	0.32	-	end	4	Membrane; multi-pass membrane protein				470
Q8K1M5 UniProt NPD GO	NPW_RAT	Neuropeptide W precursor (Preproprotein L8) (PPL8) [Contains: Neuropeptide W-23 (NPW23) (L8); Neurop ...	0.32	-	nuc	0	Secreted protein				185
P20789 UniProt NPD GO	NTR1_RAT	Neurotensin receptor type 1 (NT-R-1) (High-affinity levocabastine-insensitive neurotensin receptor) ...	0.32	-	end	6	Membrane; multi-pass membrane protein				424
P81465 UniProt NPD GO	DEF1_MESAU	Neutrophil defensin 1 (HANP-1)	0.32	-	nuc	0	Secreted protein				33
P11672 UniProt NPD GO	NGAL_MOUSE	Neutrophil gelatinase-associated lipocalin precursor (NGAL) (p25) (SV-40-induced 24P3 protein) (Lipo ...	0.32	-	exc	0	Secreted protein				200
Q969V3 UniProt NPD GO	NCLN_HUMAN	Nicalin precursor (Nicastrin-like protein)	0.32	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein		609156		563
Q91W63 UniProt NPD GO	NRK1_MOUSE	Nicotinamide riboside kinase 1 (EC 2.7.1.-)	0.32	-	cyt	0					195

You are viewing entries 38701 to 38750 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.