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
Q8AXY6 UniProt NPD GO	MUSK_CHICK	Muscle, skeletal receptor tyrosine protein kinase precursor (EC 2.7.10.1) (Muscle-specific tyrosine ...	0.40	-	end	1					947
Q9NUK0 UniProt NPD GO	MBN3_HUMAN	Muscleblind-like X-linked protein (Muscleblind-like protein 3) (Cys3His CCG1-required protein) (Prot ...	0.40	-	nuc	0	Nucleus. Cytoplasm. Greater concentration in the nucleus. In both myotonic dystrophy 1 (DM1) and DM2 ...		300413		354
Q9Z2D0 UniProt NPD GO	MTMR9_MOUSE	Myotubularin-related protein 9	0.40	-	nuc	0					545
Q58CS8 UniProt NPD GO	GNPTG_BOVIN	N-acetylglucosamine-1-phosphotransferase, subunit gamma (GlcNac-1-phosphotransferase-subunit gamma) ...	0.40	-	nuc	0	Secreted protein (By similarity). Golgi apparatus (By similarity)				282
Q5CD17 UniProt NPD GO	NAC77_ORYSA	NAC domain-containing protein 77 (ONAC077) (ONAC300)	0.40	-	nuc	0	Nucleus (Probable)				396
Q85FL6 UniProt NPD GO	NUKC_ADICA	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.40	-	nuc	0	Plastid; chloroplast				250
Q7FNR7 UniProt NPD GO	NUIC_ATRBE	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q8HVT2 UniProt NPD GO	NUIC_ENCCL	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
Q2MI46 UniProt NPD GO	NUIC_LYCES	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q3C1Q0 UniProt NPD GO	NUIC_NICSY	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q33BW8 UniProt NPD GO	NUIC_NICTO	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q85Y15 UniProt NPD GO	NUIC_PHODC	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				163
Q2MID3 UniProt NPD GO	NUIC_SOLBU	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q2VEC7 UniProt NPD GO	NUIC_SOLTU	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
P06252 UniProt NPD GO	NUIC_TOBAC	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.40	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q6FWI7 UniProt NPD GO	SIR2_CANGA	NAD-dependent histone deacetylase SIR2 (EC 3.5.1.-) (Regulatory protein SIR2) (Silent information re ...	0.40	-	cyt	0	Nucleus (By similarity)				509
Q5REN0 UniProt NPD GO	NDUBA_PONPY	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.40	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				171
Q42599 UniProt NPD GO	NUIM_ARATH	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.40	-	mit	0					222
Q9JHL1 UniProt NPD GO	NHRF2_MOUSE	Na(+)/H(+) exchange regulatory cofactor NHE-RF2 (NHERF-2) (Tyrosine kinase activator protein 1) (TKA ...	0.40	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Nucleus (By similarity). Nuc ...	apical plasma membrane [IDA]			337
P13205 UniProt NPD GO	ANFB_RAT	Natriuretic peptides B precursor (Iso-ANP) [Contains: Gamma-brain natriuretic peptide; Brain natriur ...	0.40	-	exc	0	Secreted protein				121
Q24134 UniProt NPD GO	NELFD_DROME	Negative elongation factor D	0.40	-	cyt	0	Nucleus. Associates with polytene chromosomes. Associates with the hsp70 promoter when it is inactiv ...	polytene chromosome interband [IDA] polytene chromosome puff [IDA] transcription elongation factor complex [IPI] transcriptional repressor complex [IDA]			578
P08092 UniProt NPD GO	RAN1_SCHPO	Negative regulator of sexual conjugation and meiosis (EC 2.7.11.1)	0.40	-	nuc	0					470
O08722 UniProt NPD GO	UNC5B_RAT	Netrin receptor UNC5B precursor (Unc-5 homolog B) (Unc-5 homolog 2)	0.40	-	end	1	Membrane; single-pass type I membrane protein				945
O95157 UniProt NPD GO	NXPH3_HUMAN	Neurexophilin-3 precursor	0.40	-	mit	0	Secreted protein (Potential)	extracellular region [NAS]	604636		252
Q9GLR0 UniProt NPD GO	NEC2_BOVIN	Neuroendocrine convertase 2 precursor (EC 3.4.21.94) (NEC 2) (PC2) (Prohormone convertase 2) (Propro ...	0.40	-	cyt	0	Secretory vesicle. Localized in the secretion granules (By similarity)				638
Q62889 UniProt NPD GO	NLGN3_RAT	Neuroligin-3 precursor (Gliotactin homolog)	0.40	-	end	1	Membrane; single-pass type I membrane protein (Potential)	synapse [IDA]			848
O88319 UniProt NPD GO	NTR1_MOUSE	Neurotensin receptor type 1 (NT-R-1)	0.40	+	end	6	Membrane; multi-pass membrane protein				424
Q5RC94 UniProt NPD GO	NBR1_PONPY	Next to BRCA1 gene 1 protein (Neighbor of BRCA1 gene 1 protein)	0.40	-	nuc	0					894
Q9EPA7 UniProt NPD GO	NMNA1_MOUSE	Nicotinamide mononucleotide adenylyltransferase 1 (EC 2.7.7.1) (NMN adenylyltransferase 1)	0.40	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			285
Q27521 UniProt NPD GO	NHR16_CAEEL	Nuclear hormone receptor family member nhr-16	0.40	-	mit	0	Nucleus (Potential)				388
O02305 UniProt NPD GO	NH217_CAEEL	Nuclear hormone receptor family member nhr-217	0.40	-	nuc	0	Nucleus (Potential)				372
Q9XTJ4 UniProt NPD GO	NHR3_CAEEL	Nuclear hormone receptor family member nhr-3	0.40	-	nuc	0	Nucleus (Potential)	nucleus [IC]			463
Q5VU65 UniProt NPD GO	P210L_HUMAN	Nuclear pore membrane glycoprotein 210-like precursor (Nucleoporin 210 kDa-like)	0.40	-	end	2 *	Membrane; single-pass membrane protein (Potential)				1888
Q9FGJ3 UniProt NPD GO	NFYB2_ARATH	Nuclear transcription factor Y subunit B-2 (AtNF-YB-2) (Transcriptional activator HAP3B)	0.40	-	nuc	0	Nucleus (Probable)				190
Q6RG77 UniProt NPD GO	NFYB_HORSE	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.40	-	nuc	0	Nucleus (By similarity)				207
Q9P8P7 UniProt NPD GO	NEP1_CANAL	Nucleolar essential protein 1	0.40	-	nuc	0	Nucleus; nucleolus				267
Q5RBY5 UniProt NPD GO	NDC1_PONPY	Nucleoporin NDC1 (Transmembrane protein 48)	0.40	-	end	5 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				674
Q02199 UniProt NPD GO	NUP49_YEAST	Nucleoporin NUP49/NSP49 (Nuclear pore protein NUP49/NSP49)	0.40	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear envelope [IDA] nuclear pore [IDA]			472
Q5XGN1 UniProt NPD GO	NUPL2_XENLA	Nucleoporin-like 2	0.40	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By similarity)				491
Q6P6S4 UniProt NPD GO	SIL1_RAT	Nucleotide exchange factor SIL1 precursor	0.40	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				465
Q66H86 UniProt NPD GO	OLFL1_RAT	Olfactomedin-like protein 1 precursor	0.40	-	end	0	Secreted protein (Potential)				402
P61366 UniProt NPD GO	OSTN_HUMAN	Osteocrin precursor (Musclin)	0.40	-	exc	0	Secreted protein				133
Q8BX94 UniProt NPD GO	OSBL2_MOUSE	Oxysterol-binding protein-related protein 2 (OSBP-related protein 2) (ORP-2)	0.40	-	nuc	0					484
O88436 UniProt NPD GO	PAX4_RAT	Paired box protein Pax-4	0.40	+	nuc	0	Nucleus				349
Q9PSM2 UniProt NPD GO	IPK1_STRCA	Pancreatic secretory trypsin inhibitor	0.40	-	nuc	0	Secreted protein				69
Q96QZ0 UniProt NPD GO	PANX3_HUMAN	Pannexin-3	0.40	-	end	2 *	Membrane; multi-pass membrane protein (Potential)		608422		392
O04682 UniProt NPD GO	PTI6_LYCES	Pathogenesis-related genes transcriptional activator PTI6 (PTO-interacting protein 6)	0.40	+	cyt	0	Nucleus				248
Q9QYC1 UniProt NPD GO	PCX1_MOUSE	Pecanex-like protein 1 (Pecanex homolog) (Fragment)	0.40	-	end	7	Membrane; multi-pass membrane protein (Potential)				1460
Q5AXT6 UniProt NPD GO	PPIL2_EMENI	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.40	-	nuc	0	Nucleus (By similarity)				580
Q96BP3 UniProt NPD GO	PPWD1_HUMAN	Peptidylprolyl isomerase domain and WD repeat-containing protein 1 (EC 5.2.1.8)	0.40	+	cyt	0				2A2N	646

You are viewing entries 32001 to 32050 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.