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
Q9PTS8 UniProt NPD GO	ACHA9_CHICK	Neuronal acetylcholine receptor protein subunit alpha-9 precursor (Nicotinic acetylcholine receptor ...	0.12	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				484
Q8MJV4 UniProt NPD GO	NPB_BOVIN	Neuropeptide B precursor (Preproprotein L7) (bPPL7) [Contains: Neuropeptide B-29 (NPB29) (L7C)]	0.12	-	exc	1 *	Secreted protein				122
P28674 UniProt NPD GO	NEUY_TORMA	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.12	-	cyt	1 *	Secreted protein				98
Q28602 UniProt NPD GO	NPY1R_SHEEP	Neuropeptide Y receptor type 1 (NPY1-R) (Fragment)	0.12	-	mit	2 *	Membrane; multi-pass membrane protein				116
P48145 UniProt NPD GO	NPBW1_HUMAN	Neuropeptides B/W receptor type 1 (G-protein coupled receptor 7)	0.12	-	end	5 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	600730		328
P81792 UniProt NPD GO	TX36_PHONI	Neurotoxin Tx3-6	0.12	-	nuc	0	Secreted protein				55
P07466 UniProt NPD GO	DEF6_RABIT	Neutrophil antibiotic peptide NP-5 precursor (Microbicidal peptide NP-5)	0.12	-	exc	0	Secreted protein				95
P59665 UniProt NPD GO	DEF1_HUMAN	Neutrophil defensin 1 precursor (HNP-1) (HP-1) (HP1) (Defensin, alpha 1) [Contains: HP 1-56; Neutrop ...	0.12	-	exc	0	Secreted protein		125220	1DFN	94
P59666 UniProt NPD GO	DEF3_HUMAN	Neutrophil defensin 3 precursor (HNP-3) (HP-3) (HP3) (Defensin, alpha 3) [Contains: HP 3-56; Neutrop ...	0.12	-	exc	0	Secreted protein		604522	1ZMK	94
P60032 UniProt NPD GO	DEF8_MACMU	Neutrophil defensin 8 precursor (RMAD-8)	0.12	-	exc	0	Secreted protein (By similarity)				96
Q9EP66 UniProt NPD GO	GP109_MOUSE	Nicotinic acid receptor (G-protein coupled receptor 109) (G-protein coupled receptor HM74) (Protein ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			360
P39868 UniProt NPD GO	NIA2_BRANA	Nitrate reductase [NADH], clone PBNBR1412 (EC 1.7.1.1) (NR)	0.12	-	nuc	0					911
P79292 UniProt NPD GO	OPRX_PIG	Nociceptin receptor (Orphanin FQ receptor) (Kappa-type 3 opioid receptor) (KOR-3) (ORGC) (K3 opiate ...	0.12	-	end	7	Membrane; multi-pass membrane protein				370
Q41121 UniProt NPD GO	NO30_PHAVU	Nodulin 30 precursor (30 kDa nodulin) (Npv30-1)	0.12	-	exc	0					220
Q02820 UniProt NPD GO	NCE1_YEAST	Non-classical export protein 1	0.12	-	cyt	1 *					53
Q09225 UniProt NPD GO	NRF6_CAEEL	Nose resistant to fluoxetine protein 6 precursor (Protein nrf-6)	0.12	-	end	11	Membrane; multi-pass membrane protein (Potential)				822
Q4WLM7 UniProt NPD GO	NUDF_ASPFU	Nuclear distribution protein nudF homolog	0.12	-	cyt	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				467
Q10480 UniProt NPD GO	PNU1_SCHPO	Nuclease 1, mitochondrial precursor (EC 3.1.30.-) (SpNUC1)	0.12	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			322
Q27895 UniProt NPD GO	NTP2_TOXGO	Nucleoside-triphosphatase 2 precursor (EC 3.6.1.15) (Nucleoside-triphosphatase II) (NTPase-II) (Nucl ...	0.12	-	nuc	0	Secreted protein. Found in host cell parasitophorous vacuole				628
Q9CWD8 UniProt NPD GO	NUBPL_MOUSE	Nucleotide-binding protein-like	0.12	-	mit	0					319
P31730 UniProt NPD GO	OV39_ONCVO	OV39 antigen (Fragment)	0.12	-	nuc	0					115
P81917 UniProt NPD GO	OR43A_DROME	Odorant receptor 43a	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			376
Q9V3N2 UniProt NPD GO	OR46B_DROME	Odorant receptor 46a, isoform B	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			384
P81923 UniProt NPD GO	OR59A_DROME	Odorant receptor 59a	0.12	-	mit	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			397
Q8WTE6 UniProt NPD GO	OR2_ANOGA	Odorant receptor Or2 (AgOr2)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IDA]			378
Q9GZK7 UniProt NPD GO	O11A1_HUMAN	Olfactory receptor 11A1 (Hs6M1-18)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				315
Q9GZK3 UniProt NPD GO	OR2B2_HUMAN	Olfactory receptor 2B2 (Olfactory receptor 6-1) (OR6-1) (Hs6M1-10)	0.12	-	end	8 *	Membrane; multi-pass membrane protein				357
Q8NGH3 UniProt NPD GO	OR2D3_HUMAN	Olfactory receptor 2D3	0.12	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NH16 UniProt NPD GO	OR2L2_HUMAN	Olfactory receptor 2L2 (HTPCRH07)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NG80 UniProt NPD GO	OR2L5_HUMAN	Olfactory receptor 2L5 (Olfactory receptor OR1-53)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NG83 UniProt NPD GO	OR2M3_HUMAN	Olfactory receptor 2M3 (Olfactory receptor OR1-54)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGL7 UniProt NPD GO	OR4P4_HUMAN	Olfactory receptor 4P4	0.12	-	end	6 *	Membrane; multi-pass membrane protein				312
Q8NGH5 UniProt NPD GO	O56A1_HUMAN	Olfactory receptor 56A1	0.12	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGP8 UniProt NPD GO	OR5M1_HUMAN	Olfactory receptor 5M1 (OST050)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				315
P46312 UniProt NPD GO	FAD6C_ARATH	Omega-6 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.12	+	mit	2	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein				448
P22081 UniProt NPD GO	ONCB_TAETA	Oncosphere antigen B (Fragment)	0.12	-	nuc	0					106
P25509 UniProt NPD GO	ORN2_PLAOR	Ornatin-A2	0.12	-	nuc	0	Secreted protein				41
Q8MJ50 UniProt NPD GO	OSTF1_BOVIN	Osteoclast-stimulating factor 1	0.12	-	nuc	0	Cytoplasm (By similarity)	intracellular [ISS]			214
Q4I8S2 UniProt NPD GO	OXR1_GIBZE	Oxidation resistance protein 1	0.12	-	nuc	0	Mitochondrion (By similarity)				326
P83646 UniProt NPD GO	PSBQ_ORYSA	Oxygen-evolving enhancer protein 3 (OEE3) (LP02) (Fragments)	0.12	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				22
P83288 UniProt NPD GO	TOX1_OXYKI	Oxytoxin-1 (OxyTx1)	0.12	-	nuc	0	Secreted protein	extracellular region [NAS]			69
Q53GG5 UniProt NPD GO	PDLI3_HUMAN	PDZ and LIM domain protein 3 (Actinin-associated LIM protein) (Alpha-actinin-2-associated LIM protei ...	0.12	-	nuc	0	Localizes to myofiber Z-lines		605889		364
Q66HS7 UniProt NPD GO	PDLI3_RAT	PDZ and LIM domain protein 3 (Actinin-associated LIM protein) (Alpha-actinin-2-associated LIM protei ...	0.12	-	nuc	0	Localizes to myofiber Z-lines				362
Q9NRD5 UniProt NPD GO	PICK1_HUMAN	PRKCA-binding protein (Protein kinase C-alpha-binding protein) (Protein interacting with C kinase 1) ...	0.12	-	cyt	0	Cytoplasm; perinuclear region. Also present at excitatory synapses	cytoplasm [IDA] Golgi apparatus [ISS] perinuclear region [ISS] plasma membrane [IDA] presynaptic membrane [IDA] synapse [ISS]	605926		415
Q2VL59 UniProt NPD GO	PAX9_CALGO	Paired box protein Pax-9	0.12	-	nuc	0	Nucleus				341
P55771 UniProt NPD GO	PAX9_HUMAN	Paired box protein Pax-9	0.12	-	nuc	0	Nucleus	nucleus [NAS]	604625		341
P47242 UniProt NPD GO	PAX9_MOUSE	Paired box protein Pax-9	0.12	-	nuc	0	Nucleus	transcription factor complex [TAS]			342
Q2VL54 UniProt NPD GO	PAX9_PERPO	Paired box protein Pax-9	0.12	-	nuc	0	Nucleus				341
Q2YFS2 UniProt NPD GO	PILRB_MOUSE	Paired immunoglobulin-like type 2 receptor beta precursor (Activating receptor PILR-beta) (Cell surf ...	0.12	-	end	1	Membrane; single-pass type I membrane protein (Potential)				224
Q6FW70 UniProt NPD GO	PFA3_CANGA	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.12	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				332

You are viewing entries 61551 to 61600 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.