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
Q58T61 UniProt NPD GO	M5H43_BOMMX	Maximins 5/H4 type 3 precursor [Contains: Maximin-5; Maximin-H4]	0.50	-	end	0	Secreted protein				144
Q10292 UniProt NPD GO	MEK1_SCHPO	Meiosis-specific serine/threonine-protein kinase mek1 (EC 2.7.11.1)	0.50	-	mit	0		linear element [IDA]			445
P09125 UniProt NPD GO	MSP8_EIMAC	Merozoite surface protein CMZ-8 (Fragment)	0.50	-	mit	0					259
Q6PF21 UniProt NPD GO	SYM_XENLA	Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.50	-	end	0	Cytoplasm (Probable)				905
P22438 UniProt NPD GO	SYMM_YEAST	Methionyl-tRNA synthetase, mitochondrial (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.50	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			575
P82909 UniProt NPD GO	RT36_HUMAN	Mitochondrial 28S ribosomal protein S36 (S36mt) (MRP-S36)	0.50	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA] mitochondrion [ISS]			103
Q9CQX8 UniProt NPD GO	RT36_MOUSE	Mitochondrial 28S ribosomal protein S36 (S36mt) (MRP-S36)	0.50	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [ISS] mitochondrion [IDA]			102
P58064 UniProt NPD GO	RT06_MOUSE	Mitochondrial 28S ribosomal protein S6 (S6mt) (MRP-S6)	0.50	-	nuc	0	Mitochondrion				124
Q02950 UniProt NPD GO	RT51_YEAST	Mitochondrial 40S ribosomal protein MRP51 (Mitochondrial ribosomal protein 51)	0.50	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			344
Q9C0Q7 UniProt NPD GO	TIM54_NEUCR	Mitochondrial import inner membrane translocase subunit tim-54	0.50	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				425
P26873 UniProt NPD GO	RT14_MARPO	Mitochondrial ribosomal protein S14	0.50	-	nuc	0	Mitochondrion				99
O35099 UniProt NPD GO	M3K5_MOUSE	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) (MAPK/ERK kinase kinase 5) (MEK kina ...	0.50	-	cyt	0					1380
P78595 UniProt NPD GO	CDR2_CANAL	Multidrug resistance protein CDR2	0.50	-	end	12	Membrane; multi-pass membrane protein (Potential)				1499
Q8VBX6 UniProt NPD GO	MPDZ_MOUSE	Multiple PDZ domain protein (Multi PDZ domain protein 1) (Multi-PDZ domain protein 1)	0.50	-	nuc	0	Cell membrane; cytoplasmic side. Colocalizes with HTR2C on the apical membrane of epithelial choroid ...	tight junction [IDA]			2055
O55164 UniProt NPD GO	MPDZ_RAT	Multiple PDZ domain protein (Multi PDZ domain protein 1) (Multi-PDZ domain protein 1)	0.50	-	nuc	0	Intracytoplasmic membrane. Associated with membranes. Cell membrane; cell-cell junction; tight junct ...			1Y76	2054
Q9Z1L8 UniProt NPD GO	MDS1_MOUSE	Myelodysplasia syndrome 1 protein homolog	0.50	-	nuc	0					129
P11247 UniProt NPD GO	PERM_MOUSE	Myeloperoxidase precursor (EC 1.11.1.7) (MPO) [Contains: Myeloperoxidase light chain; Myeloperoxidas ...	0.50	-	nuc	0	Lysosome				718
Q99972 UniProt NPD GO	MYOC_HUMAN	Myocilin precursor (Trabecular meshwork-induced glucocorticoid response protein)	0.50	-	mit	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...		601652		504
P15513 UniProt NPD GO	MYOM_APLCA	Myomodulin neuropeptides precursor [Contains: Myomodulin A (MM-A) (PMSMLRL-amide) (Neuron B16 peptid ...	0.50	-	exc	0	Secreted protein				370
P19706 UniProt NPD GO	MYSB_ACACA	Myosin heavy chain IB (Myosin heavy chain IL)	0.50	+	cyt	0					1147
Q28970 UniProt NPD GO	MYO7A_PIG	Myosin-7A (Myosin VIIa) (Fragment)	0.50	-	cyt	0	Cytoplasm (Probable)				566
Q9JIF9 UniProt NPD GO	MYOTI_MOUSE	Myotilin (Titin immunoglobulin domain protein) (Myofibrillar titin-like Ig domains protein)	0.50	-	nuc	0	Sarcomeric; also localized to the sarcolemma. Colocalizes with MYOZ1 at the Z-lines of skeletal musc ...				496
Q96QG7 UniProt NPD GO	MTMR9_HUMAN	Myotubularin-related protein 9	0.50	-	nuc	0			606260		549
P26645 UniProt NPD GO	MARCS_MOUSE	Myristoylated alanine-rich C-kinase substrate (MARCKS)	0.50	+	nuc	0		membrane [IDA]		1IWQ	308
P53688 UniProt NPD GO	HST4_YEAST	NAD-dependent deacetylase HST4 (EC 3.5.1.-) (Homologous to SIR2 protein 4)	0.50	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			370
Q9UNZ2 UniProt NPD GO	NSF1C_HUMAN	NSFL1 cofactor p47 (p97 cofactor p47)	0.50	-	cyt	0	Nucleus (By similarity). Predominantly nuclear in interphase cells. Bound to the axial elements of s ...		606610	1SS6	370
P97603 UniProt NPD GO	NEO1_RAT	Neogenin precursor (Fragment)	0.50	-	nuc	1	Membrane; single-pass type I membrane protein				1377
O08747 UniProt NPD GO	UNC5C_MOUSE	Netrin receptor UNC5C precursor (Unc-5 homolog C) (Unc-5 homolog 3) (Rostral cerebellar malformation ...	0.50	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)	plasma membrane [IC]			931
Q8N0W4 UniProt NPD GO	NLGNX_HUMAN	Neuroligin-4, X-linked precursor (Neuroligin X) (HNLX)	0.50	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)		300497		816
Q9BYT8 UniProt NPD GO	NEUL_HUMAN	Neurolysin, mitochondrial precursor (EC 3.4.24.16) (Neurotensin endopeptidase) (Mitochondrial oligop ...	0.50	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity). Cytoplasm (By similarity)				704
P48645 UniProt NPD GO	NEUU_HUMAN	Neuromedin U-25 precursor (NmU-25)	0.50	-	exc	1 *	Secreted protein		605103		174
P07936 UniProt NPD GO	NEUM_RAT	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43) (Protein F1)	0.50	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of growth cone and ...	growth cone [TAS]			226
O43602 UniProt NPD GO	DCX_HUMAN	Neuronal migration protein doublecortin (Lissencephalin-X) (Lis-X) (Doublin)	0.50	-	nuc	0	Cytoplasm	cytoskeleton [TAS] microtubule associated complex [TAS]	300067	1MJD	402
P25931 UniProt NPD GO	NPYR_DROME	Neuropeptide Y receptor (NPY-R) (PR4 receptor)	0.50	-	end	7	Membrane; multi-pass membrane protein				464
Q9NWW6 UniProt NPD GO	NRK1_HUMAN	Nicotinamide riboside kinase 1 (EC 2.7.1.-)	0.50	-	cyt	0			608704		199
O54842 UniProt NPD GO	NUPR1_RAT	Nuclear protein 1 (Protein p8) (Candidate of metastasis 1)	0.50	+	nuc	0	Nucleus (By similarity)				80
Q8L4B2 UniProt NPD GO	NFYC9_ARATH	Nuclear transcription factor Y subunit C-9 (AtNF-YC-9) (Transcriptional activator HAP5C)	0.50	+	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			231
P07222 UniProt NPD GO	NPM_XENLA	Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38)	0.50	-	nuc	0	Nucleus; nucleolus			1XE0	299
Q9EQW6 UniProt NPD GO	OLIG2_MOUSE	Oligodendrocyte transcription factor 2 (Oligo2)	0.50	-	nuc	0	Nucleus. Cytoplasm. The NLS contained in the bHLH domain could be masked in the native form and tran ...	cytoplasm [IDA] nucleus [IDA]			323
P18853 UniProt NPD GO	ZO8I_XENLA	Oocyte zinc finger protein XLCOF8.4I (Fragment)	0.50	-	nuc	0	Nucleus (Potential)				145
Q8CI95 UniProt NPD GO	OSB11_MOUSE	Oxysterol-binding protein-related protein 11 (OSBP-related protein 11) (ORP-11)	0.50	-	nuc	0					751
P40032 UniProt NPD GO	YEN9_YEAST	PKHD-type hydroxylase YER049W (EC 1.14.11.-)	0.50	-	nuc	0		nucleus [IDA]			644
Q9NQX0 UniProt NPD GO	PRDM6_HUMAN	PR domain zinc finger protein 6 (PR domain-containing protein 6) (Fragment)	0.50	-	nuc	0	Nucleus (Potential)				608
Q7SCY6 UniProt NPD GO	PFA4_NEUCR	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.50	+	mit	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				486
P69929 UniProt NPD GO	TXAM1_ANTMC	Peptide toxins Am 1 precursor (Peptide toxins Am I) [Contains: Peptide toxin Am 1 1 (Peptide toxin A ...	0.50	-	exc	0	Secreted protein (By similarity). Found in nematocyst (By similarity)				233
Q9JJK3 UniProt NPD GO	PEX3_CRILO	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal assembly protein PEX3)	0.50	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				373
Q9XZI6 UniProt NPD GO	PICA_CAEEL	Phosphatidylinositol-binding clathrin assembly protein unc-11 (AP180-like adaptor protein) (Uncoordi ...	0.50	-	nuc	0	Cell membrane. Clathrin-coated areas of the plasma membrane. Golgi apparatus. Colocalized with clath ...	coated pit [IDA] presynaptic membrane [IDA]			586
O19899 UniProt NPD GO	PYG_CYACA	Phycobilisome rod-core linker polypeptide cpcG	0.50	-	nuc	0	Plastid; chloroplast				234
Q8LEA8 UniProt NPD GO	EID1_ARATH	Phytochrome A-associated F-box protein (Empfindlicher im dunkelroten Licht protein 1)	0.50	-	nuc	0	Nucleus				336
P14714 UniProt NPD GO	PHYC_ARATH	Phytochrome C	0.50	-	mit	0					1111

You are viewing entries 25101 to 25150 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.