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
Q5YK03 UniProt NPD GO	MATK_VICFA	Maturase K (Intron maturase)	0.65	-	cyt	0	Plastid; chloroplast				503
O44740 UniProt NPD GO	MEI2_CAEEL	Meiotic spindle formation protein 2	0.65	-	nuc	0	Localized to the spindle poles and condensed chromatin during female meiosis. Also localized to the ...				280
O60732 UniProt NPD GO	MAGC1_HUMAN	Melanoma-associated antigen C1 (MAGE-C1 antigen) (Cancer-testis antigen CT7)	0.65	-	nuc	0			300223		1142
Q7T105 UniProt NPD GO	MIER1_XENLA	Mesoderm induction early response protein 1 (Mi-er1) (Xmi-er1) (Early response 1) (Er1)	0.65	-	nuc	0	Nucleus				495
O88368 UniProt NPD GO	MITF_RAT	Microphthalmia-associated transcription factor (Fragment)	0.65	+	nuc	0	Nucleus				110
Q865F1 UniProt NPD GO	MTP_PIG	Microsomal triglyceride transfer protein large subunit precursor	0.65	-	exc	0	Endoplasmic reticulum (By similarity)				894
O15344 UniProt NPD GO	TRI18_HUMAN	Midline-1 (EC 6.3.2.-) (Tripartite motif-containing protein 18) (Putative transcription factor XPRF) ...	0.65	-	nuc	0	Cytoplasm. Microtubule-associated. It is associated with microtubules throughout the cell cycle, co- ...	microtubule associated complex [TAS]	300000	2FFW	667
P82458 UniProt NPD GO	TRI18_RAT	Midline-1 (Tripartite motif-containing protein 18)	0.65	-	nuc	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)				667
Q9UJV3 UniProt NPD GO	TRIM1_HUMAN	Midline-2 (Midline defect 2) (Tripartite motif-containing protein 1) (Midin-2) (RING finger protein ...	0.65	-	nuc	0	Cytoplasm. Microtubule-associated	microtubule associated complex [NAS]	300204		715
Q9C107 UniProt NPD GO	MCL1_SCHPO	Minichromosome loss protein 1	0.65	-	mit	0	Nucleus	alpha DNA polymerase:primase complex [IDA]			815
Q10241 UniProt NPD GO	CMB1_SCHPO	Mismatch-binding protein cmb1	0.65	-	nuc	0	Nucleus (Potential)				223
P38880 UniProt NPD GO	MDM31_YEAST	Mitochondrial distribution and morphology protein 31, mitochondrial precursor	0.65	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] nucleus [IDA]			579
Q95869 UniProt NPD GO	RT12_NICSY	Mitochondrial ribosomal protein S12	0.65	-	nuc	0	Mitochondrion				125
P14875 UniProt NPD GO	RT14_OENBE	Mitochondrial ribosomal protein S14	0.65	-	nuc	0	Mitochondrion				99
Q75KK8 UniProt NPD GO	MPK14_ORYSA	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (MAP kinase 14)	0.65	-	nuc	0					542
Q9SJG9 UniProt NPD GO	MPK20_ARATH	Mitogen-activated protein kinase 20 (EC 2.7.11.24) (MAP kinase 20) (AtMPK20)	0.65	-	nuc	0					606
O14940 UniProt NPD GO	MOS1A_HUMAN	Molybdenum cofactor biosynthesis protein 1 A (MOCS1A)	0.65	-	mit	0		nucleus [NAS]	603707		385
O35182 UniProt NPD GO	SMAD6_MOUSE	Mothers against decapentaplegic homolog 6 (SMAD 6) (Mothers against DPP homolog 6) (Smad6) (Mad homo ...	0.65	-	nuc	0					495
O43541 UniProt NPD GO	SMAD6_HUMAN	Mothers against decapentaplegic homolog 6 (SMAD 6) (Mothers against DPP homolog 6) (Smad6) (hSMAD6)	0.65	-	nuc	0			602931		496
Q5KJL5 UniProt NPD GO	MRD1_CRYNE	Multiple RNA-binding domain-containing protein 1	0.65	-	cyt	0	Nucleus (By similarity)				769
Q7Z7M0 UniProt NPD GO	MEGF8_HUMAN	Multiple epidermal growth factor-like domains 8 (EGF-like domain-containing protein 4) (Multiple EGF ...	0.65	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)		604267		2386
P16395 UniProt NPD GO	ACM1_DROME	Muscarinic acetylcholine receptor DM1	0.65	-	end	7	Membrane; multi-pass membrane protein	plasma membrane [NAS]			805
Q12175 UniProt NPD GO	MSH5_YEAST	MutS protein homolog 5	0.65	-	mit	0		nucleus [IDA]			901
P11778 UniProt NPD GO	MYH7_PAPHA	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta) (Fragment)	0.65	-	nuc	0	Thick filaments of the myofibrils				244
O00308 UniProt NPD GO	WWP2_HUMAN	NEDD4-like E3 ubiquitin-protein ligase WWP2 (EC 6.3.2.-) (WW domain-containing protein 2) (Atrophin- ...	0.65	-	nuc	0		ubiquitin ligase complex [TAS]	602308		870
Q6P7H4 UniProt NPD GO	NIPA_XENLA	NIPA-like protein (Zinc finger C3HC-type protein 1-like)	0.65	-	nuc	0	Nucleus (By similarity)				477
Q5R7G9 UniProt NPD GO	NUAK2_PONPY	NUAK family SNF1-like kinase 2 (EC 2.7.11.1)	0.65	-	nuc	0					628
Q9HD90 UniProt NPD GO	NDF4_HUMAN	Neurogenic differentiation factor 4 (NeuroD4)	0.65	-	nuc	0	Nucleus (Potential)				331
P31695 UniProt NPD GO	NOTC4_MOUSE	Neurogenic locus notch homolog protein 4 precursor (Notch 4) [Contains: Transforming protein Int-3; ...	0.65	-	nuc	0	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	cell surface [ISS] integral to plasma membrane [ISS] nucleus [ISS]			1964
O54705 UniProt NPD GO	NOS2_CAVPO	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.65	-	cyt	0		cytosol [ISS]			1149
Q06518 UniProt NPD GO	NOS2_RAT	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.65	-	mit	0		cytosol [ISS]			1147
P12902 UniProt NPD GO	HM14A_CHICK	Nonhistone chromosomal protein HMG-14A	0.65	+	nuc	0	Nucleus				104
O45449 UniProt NPD GO	NH108_CAEEL	Nuclear hormone receptor family member nhr-108	0.65	-	nuc	0	Nucleus (Potential)				338
P91829 UniProt NPD GO	NHR69_CAEEL	Nuclear hormone receptor family member nhr-69	0.65	-	nuc	0	Nucleus (Potential)				373
Q8R3G1 UniProt NPD GO	PP1R8_MOUSE	Nuclear inhibitor of protein phosphatase 1 (NIPP-1) (Protein phosphatase 1 regulatory inhibitor subu ...	0.65	+	nuc	0	Nucleus (By similarity). Mainly, but not exclusively, nuclear. Nucleus; nucleoplasm; nuclear speckle ...				351
Q12972 UniProt NPD GO	PP1R8_HUMAN	Nuclear inhibitor of protein phosphatase 1 (NIPP-1) (Protein phosphatase 1 regulatory inhibitor subu ...	0.65	+	nuc	0	Nucleus. Primarily, but not exclusively, nuclear. Nucleus; nucleoplasm; nuclear speckle. Isoform Gam ...	nucleus [TAS]	602636		351
Q9Y266 UniProt NPD GO	NUDC_HUMAN	Nuclear migration protein nudC (Nuclear distribution protein C homolog)	0.65	-	nuc	0	Cytoplasm. In a filamentous pattern adjacent to the nucleus of migrating cerebellar granule cells. C ...				331
P17955 UniProt NPD GO	NUP62_RAT	Nuclear pore glycoprotein p62 (62 kDa nucleoporin)	0.65	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex. Central region of the nuclear pore, within the tran ...	cytoplasm [ISS] nuclear pore [ISS] nucleocytoplasmic shuttling complex [ISS]			525
Q84JP1 UniProt NPD GO	NFYA7_ARATH	Nuclear transcription factor Y subunit A-7 (AtNF-YA-7)	0.65	-	nuc	0	Nucleus (Probable)				190
O17580 UniProt NPD GO	NOC2L_CAEEL	Nucleolar complex protein 2 homolog (Protein NOC2 homolog)	0.65	+	nuc	0	Nucleus (By similarity)				715
Q9H6R4 UniProt NPD GO	NOL6_HUMAN	Nucleolar protein 6 (Nucleolar RNA-associated protein) (Nrap)	0.65	-	nuc	0	Nucleus; nucleolus. Localizes to condensed chromosomes in mitosis (By similarity)	condensed nuclear chromosome [ISS] nucleolus [ISS] small nucleolar ribonucleoprotein complex [ISS]			1146
Q8R5K4 UniProt NPD GO	NOL6_MOUSE	Nucleolar protein 6 (Nucleolar RNA-associated protein) (Nrap)	0.65	-	nuc	0	Nucleus; nucleolus. Localizes to condensed chromosomes in mitosis	condensed nuclear chromosome [IDA] nucleolus [IDA] small nucleolar ribonucleoprotein complex [ISS]			1141
P49687 UniProt NPD GO	NU145_YEAST	Nucleoporin NUP145 precursor (EC 3.4.21.-) (Nuclear pore protein NUP145) [Contains: Nucleoporin NUP1 ...	0.65	-	mit	0	NUP145C: Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. NUP145C, NUP145N: Nucleu ...	nuclear pore [IDA]			1317
Q16625 UniProt NPD GO	OCLN_HUMAN	Occludin	0.65	-	end	5	Membrane; multi-pass membrane protein	plasma membrane [TAS]	602876		522
Q5R923 UniProt NPD GO	OPTN_PONPY	Optineurin	0.65	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus (By similarity). Found in the perinuc ...				527
Q24432 UniProt NPD GO	OMB_DROME	Optomotor-blind protein (Lethal(1)optomotor-blind) (L(1)omb) (Protein bifid)	0.65	-	nuc	0	Nucleus (Potential)				972
Q9HFU9 UniProt NPD GO	OAZ_SCHJP	Ornithine decarboxylase antizyme (ODC-Az)	0.65	-	nuc	0					226
Q12202 UniProt NPD GO	OSW2_YEAST	Outer spore wall protein 2	0.65	-	nuc	0	Cytoplasm. In mature spores. Localized around the prospore membrane during meiosis II	cytoplasm [IDA] prospore membrane [IDA]			724
Q9TSV5 UniProt NPD GO	PO5F1_PIG	POU domain, class 5, transcription factor 1 (Octamer-binding transcription factor 3) (Oct-3) (Oct-4) ...	0.65	+	cyt	0	Nucleus (By similarity)				360
Q90268 UniProt NPD GO	PAX2A_BRARE	Paired box protein Pax-2a (Pax[Zf-b]) (No isthmus protein)	0.65	-	nuc	0	Nucleus	nucleus [NAS]			410

You are viewing entries 16451 to 16500 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.