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)

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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
Q61161 UniProt NPD GO	M4K2_MOUSE	Mitogen-activated protein kinase kinase kinase kinase 2 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.76	-	cyt	0	Cytoplasm. Cell membrane; basolateral cell membrane; peripheral membrane protein. Golgi apparatus; G ...				821
O08901 UniProt NPD GO	BUB1_MOUSE	Mitotic checkpoint serine/threonine-protein kinase BUB1 (EC 2.7.11.1) (MBUB1) (BUB1A)	0.76	-	nuc	0	Nucleus. Nuclear in interphase cells. Kinetochore localization is required for normal mitotic timing ...	kinetochore [IDA]			1058
Q9R0Q4 UniProt NPD GO	MO4L2_MOUSE	Mortality factor 4-like protein 2 (MORF-related gene X protein) (Transcription factor-like protein M ...	0.76	-	nuc	0	Nucleus (By similarity)				288
P10242 UniProt NPD GO	MYB_HUMAN	Myb proto-oncogene protein (C-myb)	0.76	+	nuc	0	Nucleus	nuclear matrix [NAS]	189990		640
P04198 UniProt NPD GO	MYCN_HUMAN	N-myc proto-oncogene protein	0.76	+	nuc	0	Nucleus	chromatin [TAS] nucleus [IDA]	164840		464
Q9C5W3 UniProt NPD GO	NADK2_ARATH	NAD kinase 2, chloroplast precursor (EC 2.7.1.23) (AtNADK-2)	0.76	-	mit	0	Plastid; chloroplast				985
Q5R4J9 UniProt NPD GO	NARG1_PONPY	NMDA receptor-regulated protein 1	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic, nuclear in some cases (By si ...				866
Q9BXJ9 UniProt NPD GO	NARG1_HUMAN	NMDA receptor-regulated protein 1 (N-terminal acetyltransferase) (Tubedown-1 protein) (Tbdn100) (Gas ...	0.76	-	nuc	0	Cytoplasm. Nucleus. Mainly cytoplasmic, nuclear in some cases. Present in the free cytosolic and cyt ...	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IDA]	608000		866
P10676 UniProt NPD GO	NINAC_DROME	Neither inactivation nor afterpotential protein C (EC 2.7.11.1)	0.76	+	nuc	0	Cytoplasm. Cytoskeleton	cytoplasm [IDA] inaD signaling complex [TAS] myosin III [NAS]			1501
P59240 UniProt NPD GO	NPHP4_MOUSE	Nephrocystin-4 (Nephroretinin)	0.76	-	nuc	0		membrane [ISS]			1425
Q6R891 UniProt NPD GO	NEB2_MOUSE	Neurabin-2 (Neurabin-II) (Spinophilin) (Protein phosphatase 1 regulatory subunit 9B)	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Enriched at synapse and cadherin-based cell-cell ...	cortical actin cytoskeleton [IDA] filopodium [IDA]			817
P02547 UniProt NPD GO	NFL_PIG	Neurofilament triplet L protein (68 kDa neurofilament protein) (Neurofilament light polypeptide) (NF ...	0.76	-	nuc	0					548
Q62414 UniProt NPD GO	NDF2_MOUSE	Neurogenic differentiation factor 2 (NeuroD2) (NeuroD-related factor) (NDRF)	0.76	+	nuc	0	Nucleus (Probable)				383
P46531 UniProt NPD GO	NOTC1_HUMAN	Neurogenic locus notch homolog protein 1 precursor (Notch 1) (hN1) (Translocation-associated notch p ...	0.76	+	exc	0	Cell membrane; single-pass type I membrane protein (By similarity). NICD: Nucleus (By similarity). F ...	integral to membrane [NAS] nucleus [TAS]	190198	2F8Y	2556
Q9Y4Z2 UniProt NPD GO	NGN3_HUMAN	Neurogenin 3	0.76	-	nuc	0	Nucleus (Potential)		604882		214
Q8R4I7 UniProt NPD GO	NETO1_MOUSE	Neuropilin and tolloid-like protein 1 precursor (Brain-specific transmembrane protein containing 2 C ...	0.76	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				533
Q9BZQ8 UniProt NPD GO	NIBA_HUMAN	Niban protein	0.76	-	nuc	0					928
Q8R1F1 UniProt NPD GO	NIBL_MOUSE	Niban-like protein	0.76	-	nuc	0					749
P29477 UniProt NPD GO	NOS2_MOUSE	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.76	-	cyt	0		cortical cytoskeleton [IDA] cytoplasm [IDA] cytosol [TAS] perinuclear region [IDA]		3NOD	1144
Q62923 UniProt NPD GO	PNOC_RAT	Nociceptin precursor [Contains: Neuropeptide 1; Nociceptin (Orphanin FQ) (PPNOC) (ORL1 receptor agon ...	0.76	-	exc	0	Secreted protein				181
Q13519 UniProt NPD GO	PNOC_HUMAN	Nociceptin precursor [Contains: Neuropeptide 1; Nociceptin (Orphanin FQ) (PPNOC); Neuropeptide 2]	0.76	-	exc	0	Secreted protein	extracellular region [TAS]	601459		176
Q9W741 UniProt NPD GO	NOGG1_BRARE	Noggin-1 precursor	0.76	-	exc	0	Secreted protein				216
Q3KNJ2 UniProt NPD GO	NHEJ1_MOUSE	Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)	0.76	-	nuc	0	Nucleus (By similarity)				295
Q5ZJZ6 UniProt NPD GO	NCBP1_CHICK	Nuclear cap-binding protein subunit 1	0.76	+	mit	0	Nucleus (By similarity)				793
Q4P0N6 UniProt NPD GO	NDE1_USTMA	Nuclear distribution protein nudE homolog 1	0.76	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules (By similarity)				646
O13961 UniProt NPD GO	NDC1_SCHPO	Nuclear envelope protein ndc1 (Cell untimely torn protein 11)	0.76	-	end	7 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...	nuclear membrane [IDA] spindle pole body [IDA]			601
Q00653 UniProt NPD GO	NFKB2_HUMAN	Nuclear factor NF-kappa-B p100 subunit (DNA-binding factor KBF2) (H2TF1) (Lymphocyte translocation c ...	0.76	-	nuc	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...	cytoplasm [IDA] nucleus [IDA]	164012	1A3Q	899
O17657 UniProt NPD GO	NH164_CAEEL	Nuclear hormone receptor family member nhr-164	0.76	-	cyt	0	Nucleus (Potential)				389
Q7SHR8 UniProt NPD GO	NOG2_NEUCR	Nucleolar GTP-binding protein 2	0.76	-	nuc	0	Nucleus; nucleolus (By similarity)				619
O60936 UniProt NPD GO	NOL3_HUMAN	Nucleolar protein 3 (Apoptosis repressor with CARD) (Muscle-enriched cytoplasmic protein) (Myp) (Nuc ...	0.76	-	nuc	0	Isoform 1: Nucleus; nucleoplasm; nucleolus. Isoform 2: Cytoplasm	cytosol [TAS] nucleolus [TAS]	605235		219
P40064 UniProt NPD GO	NU157_YEAST	Nucleoporin NUP157 (Nuclear pore protein NUP157)	0.76	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			1391
P40368 UniProt NPD GO	NUP82_YEAST	Nucleoporin NUP82 (Nuclear pore protein NUP82)	0.76	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side	nuclear pore [IDA]			713
Q86X67 UniProt NPD GO	NUD13_HUMAN	Nucleoside diphosphate linked moiety X motif 13 (EC 3.-.-.-) (Nudix motif 13)	0.76	-	mit	0			609233		352
Q6NUA7 UniProt NPD GO	SIL1_XENLA	Nucleotide exchange factor SIL1 precursor	0.76	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				456
Q5RI56 UniProt NPD GO	OPTN_BRARE	Optineurin	0.76	-	nuc	0	Cytoplasm (By similarity)				517
Q8SQ01 UniProt NPD GO	PXR_MACMU	Orphan nuclear receptor PXR (Pregnane X receptor)	0.76	-	cyt	0	Nucleus (By similarity)				434
Q9Z1B8 UniProt NPD GO	PHF1_MOUSE	PHD finger protein 1 (Protein PHF1) (T-complex testis-expressed 3) (Polycomblike 1) (mPCl1)	0.76	-	nuc	0	Nucleus (Potential)				559
Q6NWE1 UniProt NPD GO	PHF10_BRARE	PHD finger protein 10	0.76	-	nuc	0	Nucleus (Probable)				408
Q5TYW8 UniProt NPD GO	PRAM3_HUMAN	PRAME family member 3	0.76	+	cyt	0					479
P47238 UniProt NPD GO	PAX6_COTJA	Paired box protein Pax-6 (Pax-QNR)	0.76	+	nuc	0	Nucleus				416
Q7RTS3 UniProt NPD GO	PTF1A_HUMAN	Pancreas transcription factor 1 subunit alpha (Pancreas-specific transcription factor 1a) (bHLH tran ...	0.76	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In chronic pancreatitis associated with pancreas ...	cytoplasm [ISS] nucleus [ISS] transcription factor complex [ISS]	609069		328
Q5ARI5 UniProt NPD GO	PPIL4_EMENI	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.76	+	nuc	0	Nucleus (By similarity)				461
O54943 UniProt NPD GO	PER2_MOUSE	Period circadian protein 2 (mPER2)	0.76	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IPI]			1257
O00541 UniProt NPD GO	PESC_HUMAN	Pescadillo homolog 1	0.76	+	cyt	0	Nucleus; nucleolus		605819		588
Q9EQ61 UniProt NPD GO	PESC_MOUSE	Pescadillo homolog 1	0.76	+	cyt	0	Nucleus; nucleolus	condensed chromosome [IDA] nucleolus [IDA] nucleus [IDA]			584
P35911 UniProt NPD GO	APCE_GALSU	Phycobilisome linker polypeptide (Anchor polypeptide) (PBS-anchor protein)	0.76	-	nuc	0	Plastid; chloroplast				863
Q9ZP54 UniProt NPD GO	PARP1_ARATH	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT 1) (NAD(+) ADP-ribosyltransferase 1) (P ...	0.76	-	nuc	0	Nucleus (Potential)			1V9X	983
Q9UT49 UniProt NPD GO	CID13_SCHPO	Poly(A) polymerase cid13 (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase)	0.76	-	nuc	0	Cytoplasm	cytoplasm [IDA]			578
Q9NTG1 UniProt NPD GO	PKDRE_HUMAN	Polycystic kidney disease and receptor for egg jelly-related protein precursor (PKD and REJ homolog) ...	0.76	-	end	13	Membrane; multi-pass membrane protein (Potential)	membrane [TAS]	604670		2253
O35984 UniProt NPD GO	PBX2_MOUSE	Pre-B-cell leukemia transcription factor 2 (Homeobox protein PBX2)	0.76	-	nuc	0	Nucleus (Probable)				430

You are viewing entries 10951 to 11000 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.