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
O00562 UniProt NPD GO	PITM1_HUMAN	Membrane-associated phosphatidylinositol transfer protein 1 (Phosphatidylinositol transfer protein, ...	0.60	-	nuc	0	Cytoplasm. Peripheral membrane protein associated with Golgi stacks in interphase cells. A minor pro ...	membrane fraction [TAS]	608794		1243
Q61847 UniProt NPD GO	MEP1B_MOUSE	Meprin A subunit beta precursor (EC 3.4.24.18) (Endopeptidase-2)	0.60	-	end	1	Membrane; single-pass type I membrane protein				704
Q5R6F1 UniProt NPD GO	MESD2_PONPY	Mesoderm development candidate 2	0.60	+	exc	0					234
Q8C7H1 UniProt NPD GO	MMAA_MOUSE	Methylmalonic aciduria type A homolog, mitochondrial precursor	0.60	-	mit	0	Mitochondrion (By similarity)				415
Q3SZP2 UniProt NPD GO	MARE2_BOVIN	Microtubule-associated protein RP/EB family member 2	0.60	-	nuc	0	Cytoplasm (By similarity). Associated with the microtubule network. Accumulates at the plus end of m ...				326
Q3B8Q0 UniProt NPD GO	MARE2_RAT	Microtubule-associated protein RP/EB family member 2	0.60	-	nuc	0	Cytoplasm (By similarity). Associated with the microtubule network. Accumulates at the plus end of m ...				326
P82929 UniProt NPD GO	RT34_BOVIN	Mitochondrial 28S ribosomal protein S34 (S34mt) (MRP-S34)	0.60	-	mit	0	Mitochondrion				218
Q75B48 UniProt NPD GO	RT51_ASHGO	Mitochondrial 40S ribosomal protein MRP51 (Mitochondrial ribosomal protein 51)	0.60	-	nuc	0	Mitochondrion (By similarity)				360
Q99MB2 UniProt NPD GO	MTFR1_MOUSE	Mitochondrial fission regulator 1	0.60	-	mit	0	Mitochondrion (By similarity)				328
Q9LUC3 UniProt NPD GO	MPK19_ARATH	Mitogen-activated protein kinase 19 (EC 2.7.11.24) (MAP kinase 19) (AtMPK19)	0.60	-	nuc	0					593
Q7SG09 UniProt NPD GO	MRD1_NEUCR	Multiple RNA-binding domain-containing protein 1	0.60	-	cyt	0	Nucleus (By similarity)				827
Q9JK37 UniProt NPD GO	MYOZ1_MOUSE	Myozenin-1 (Calsarcin-2) (Filamin-, actinin- and telethonin-binding protein) (Protein FATZ)	0.60	-	nuc	0	Localized to the nucleus and pseudopodia of undifferentiated cells and detected throughout the myotu ...	actin cytoskeleton [IDA]			296
Q64210 UniProt NPD GO	MYC2_SPEBE	N-myc 2 proto-oncogene protein	0.60	+	nuc	0	Nucleus (Potential)				454
Q6L395 UniProt NPD GO	NUKC_SACHY	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.60	-	nuc	0	Plastid; chloroplast				248
Q6ENV9 UniProt NPD GO	NUKC_SACOF	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.60	-	nuc	0	Plastid; chloroplast				248
O59923 UniProt NPD GO	SIR2_CANAL	NAD-dependent histone deacetylase SIR2 (EC 3.5.1.-) (Regulatory protein SIR2) (Silent information re ...	0.60	-	nuc	0	Nucleus (By similarity)				515
P33327 UniProt NPD GO	DHE2_YEAST	NAD-specific glutamate dehydrogenase (EC 1.4.1.2) (NAD-GDH)	0.60	-	cyt	0		mitochondrion [IDA] soluble fraction [IDA]			1092
Q95748 UniProt NPD GO	NUGM_ARATH	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.60	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				190
Q863H2 UniProt NPD GO	NCTR1_BOVIN	Natural cytotoxicity triggering receptor 1 precursor (Natural killer cell p46-related protein) (NKp4 ...	0.60	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				308
Q64322 UniProt NPD GO	NPDC1_MOUSE	Neural proliferation differentiation and control protein 1 precursor (NPDC-1 protein)	0.60	-	mit	1 *					332
P10041 UniProt NPD GO	DL_DROME	Neurogenic locus protein delta precursor	0.60	-	mit	1 *	Membrane; single-pass type I membrane protein	integral to membrane [TAS] plasma membrane [IDA]			833
P42676 UniProt NPD GO	NEUL_RAT	Neurolysin, mitochondrial precursor (EC 3.4.24.16) (Neurotensin endopeptidase) (Mitochondrial oligop ...	0.60	-	mit	0	Mitochondrion; mitochondrial intermembrane space. Cytoplasm			1I1I	704
Q9D3P9 UniProt NPD GO	NEUT_MOUSE	Neurotensin/neuromedin N precursor [Contains: Large neuromedin N (NmN-125); Neuromedin N (NmN) (NN); ...	0.60	-	exc	0	Secreted protein (By similarity). Packaged within secretory vesicles (By similarity)				169
O93525 UniProt NPD GO	NOGG_CHICK	Noggin precursor (cNoggin)	0.60	-	nuc	0	Secreted protein				223
P05114 UniProt NPD GO	HMGN1_HUMAN	Nonhistone chromosomal protein HMG-14 (High-mobility group nucleosome-binding domain-containing prot ...	0.60	-	nuc	0	Nucleus	chromatin [TAS]	163920		99
Q6BJE2 UniProt NPD GO	NMD4_DEBHA	Nonsense-mediated decay protein 4	0.60	-	nuc	0	Cytoplasm (By similarity)				416
Q9N1Q7 UniProt NPD GO	SP100_PANTR	Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Fragment)	0.60	+	nuc	0	Nucleus (By similarity). Found in the nuclear body, a nucleoplasmic structure of punctate shape, whi ...				215
Q66JL0 UniProt NPD GO	NDE1_XENTR	Nuclear distribution protein nudE homolog 1	0.60	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				349
Q04861 UniProt NPD GO	NFKB1_CHICK	Nuclear factor NF-kappa-B p105 subunit [Contains: Nuclear factor NF-kappa-B p50 subunit]	0.60	+	cyt	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...				984
O16359 UniProt NPD GO	NH103_CAEEL	Nuclear hormone receptor family member nhr-103	0.60	-	nuc	0	Nucleus (Potential)				394
O17082 UniProt NPD GO	NH125_CAEEL	Nuclear hormone receptor family member nhr-125	0.60	-	mit	0	Nucleus (Potential)				399
P37199 UniProt NPD GO	NU155_RAT	Nuclear pore complex protein Nup155 (Nucleoporin Nup155) (155 kDa nucleoporin) (P140)	0.60	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; peripheral membrane protein; cytoplasmic side. Nucl ...				1390
Q9EPU2 UniProt NPD GO	NCOA3_RAT	Nuclear receptor coactivator 3 (EC 2.3.1.48) (NCoA-3) (Amplified in breast cancer-1 protein homolog) ...	0.60	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic and weakly nuclear. Upon TNF ...				1082
Q16656 UniProt NPD GO	NRF1_HUMAN	Nuclear respiratory factor 1 (NRF-1) (Alpha palindromic-binding protein) (Alpha-pal)	0.60	-	cyt	0	Nucleus		600879		503
Q8LFU0 UniProt NPD GO	NFYAA_ARATH	Nuclear transcription factor Y subunit A-10 (AtNF-YA-10)	0.60	-	nuc	0	Nucleus (Probable)				269
Q67XJ2 UniProt NPD GO	NFYBA_ARATH	Nuclear transcription factor Y subunit B-10 (AtNF-YB-10)	0.60	-	nuc	0	Nucleus (Probable)				176
Q02931 UniProt NPD GO	NAN1_YEAST	Nucleolar protein NAN1 (U3 small nucleolar RNA-associated protein 17) (U3 snoRNA-associated protein ...	0.60	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			896
Q12499 UniProt NPD GO	NOP58_YEAST	Nucleolar protein NOP58 (Nucleolar protein NOP5)	0.60	+	nuc	0	Nucleus; nucleolus	nucleolus [IEP] small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [IPI]			511
Q9V4W1 UniProt NPD GO	GLE1_DROME	Nucleoporin GLE1	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	mitochondrion [ISS] nuclear pore [ISS]			677
Q6AX31 UniProt NPD GO	NDC1_XENLA	Nucleoporin NDC1 (xNDC1) (Transmembrane protein 48)	0.60	-	end	4 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				660
Q6UWY5 UniProt NPD GO	OLFL1_HUMAN	Olfactomedin-like protein 1 precursor	0.60	-	end	0	Secreted protein (Potential)				402
P53346 UniProt NPD GO	ONCM_BOVIN	Oncostatin M precursor (OSM)	0.60	-	nuc	0	Secreted protein				245
Q9YHY9 UniProt NPD GO	OTC_CHICK	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.60	+	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial matrix [ISS]			354
Q505F1 UniProt NPD GO	TR2_MOUSE	Orphan nuclear receptor TR2 (Testicular receptor 2) (mTR2)	0.60	+	nuc	0	Nucleus (Potential)	nucleus [IC]			590
P39928 UniProt NPD GO	SLN1_YEAST	Osmolarity two-component system protein SLN1 (EC 2.7.13.3)	0.60	-	end	2 *	Membrane; multi-pass membrane protein (Potential)			1OXK	1220
Q8K561 UniProt NPD GO	OTOAN_MOUSE	Otoancorin precursor	0.60	-	cyt	0	Cell membrane; apical cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). At the ...	apical plasma membrane [IDA]			1137
Q9NLA6 UniProt NPD GO	OAF_DROME	Out at first protein [Contains: Out at first short protein]	0.60	-	nuc	0					487
Q9EQ09 UniProt NPD GO	OLR1_MOUSE	Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) (Lectin-type oxidized LDL receptor 1 ...	0.60	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Secreted protein (By similarity ...	extrinsic to plasma membrane [TAS]			363
P21952 UniProt NPD GO	PO3F1_MOUSE	POU domain, class 3, transcription factor 1 (Octamer-binding transcription factor 6) (Oct-6) (POU-do ...	0.60	+	cyt	0	Nucleus	nucleus [IDA]			449
O18381 UniProt NPD GO	PAX6_DROME	Paired box protein Pax-6 (Protein eyeless)	0.60	+	nuc	0	Nucleus	nucleus [TAS]			857

You are viewing entries 19151 to 19200 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.