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
Q9VGP2 UniProt NPD GO	NINAG_DROME	Neither inactivation nor afterpotential protein G precursor (EC 1.-.-.-)	0.23	-	end	1 *	Secreted protein (Potential)				581
Q9JLB5 UniProt NPD GO	ACH10_RAT	Neuronal acetylcholine receptor protein subunit alpha-10 precursor (Nicotinic acetylcholine receptor ...	0.23	-	end	4	Membrane; multi-pass membrane protein (Probable)	nicotinic acetylcholine-gated receptor-chan... [IEP]			447
Q15818 UniProt NPD GO	NPTX1_HUMAN	Neuronal pentraxin-1 precursor (NP1) (Neuronal pentraxin I) (NP-I)	0.23	-	exc	0	Secretory vesicle (Potential)		602367		432
Q03696 UniProt NPD GO	NGCA_CHICK	Neuronal-glial cell adhesion molecule precursor (Ng-CAM)	0.23	+	end	1 *	Membrane; single-pass type I membrane protein				1266
O02813 UniProt NPD GO	NPY1R_CANFA	Neuropeptide Y receptor type 1 (NPY1-R)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				382
P25929 UniProt NPD GO	NPY1R_HUMAN	Neuropeptide Y receptor type 1 (NPY1-R)	0.23	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	162641		384
Q63384 UniProt NPD GO	NTR2_RAT	Neurotensin receptor type 2 (NT-R-2) (High-affinity levocabastine-sensitive neurotensin receptor)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				416
P83919 UniProt NPD GO	TX13A_CUPSA	Neurotoxic enhancer CSTX-13 A chain	0.23	-	nuc	0	Secreted protein				34
P39863 UniProt NPD GO	NIA_FUSOX	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.23	-	nuc	0					905
Q92037 UniProt NPD GO	NOS2_CARAU	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.23	-	mit	0					164
Q8BM13 UniProt NPD GO	NOE2_MOUSE	Noelin-2 precursor (Olfactomedin-2)	0.23	-	mit	0	Secreted protein (By similarity)				448
Q12207 UniProt NPD GO	NCE2_YEAST	Non-classical export protein 2	0.23	-	end	4 *	Membrane; multi-pass membrane protein	cytoplasm [IDA] endoplasmic reticulum [IDA] mitochondrion [IDA]			173
P82353 UniProt NPD GO	NLTP2_PRUAR	Nonspecific lipid-transfer protein 2 (LTP 2)	0.23	-	nuc	0					68
Q753J1 UniProt NPD GO	NCA2_ASHGO	Nuclear control of ATPase protein 2	0.23	-	nuc	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				569
Q9P869 UniProt NPD GO	SNF4_KLULA	Nuclear protein SNF4	0.23	-	mit	0	Nucleus (By similarity)				328
Q9SFD8 UniProt NPD GO	NFYB9_ARATH	Nuclear transcription factor Y subunit B-9 (AtNF-YB-9) (Protein LEAFY COTYLEDON 1)	0.23	-	nuc	0	Nucleus (Probable)				208
P52912 UniProt NPD GO	TIA1_MOUSE	Nucleolysin TIA-1 (RNA-binding protein TIA-1)	0.23	-	cyt	0	Cytoplasmic granule (By similarity). Cytoplasmic granules of cytolytic T-lymphocytes (By similarity) ...	cytoplasm [IDA] nucleus [IDA]			386
P70318 UniProt NPD GO	TIAR_MOUSE	Nucleolysin TIAR (TIA-1-related protein)	0.23	-	cyt	0		cytoplasm [TAS]			392
Q9VCG4 UniProt NPD GO	NDC1_DROME	Nucleoporin Ndc1	0.23	-	end	7 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				578
P47923 UniProt NPD GO	NDK2_PEA	Nucleoside diphosphate kinase 2, chloroplast precursor (EC 2.7.4.6) (Nucleoside diphosphate kinase I ...	0.23	-	mit	0	Plastid; chloroplast (Potential)				230
P81921 UniProt NPD GO	OR47A_DROME	Odorant receptor 47a	0.23	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			385
Q9TQX4 UniProt NPD GO	OR1E2_GORGO	Olfactory receptor 1E2	0.23	-	end	6 *	Membrane; multi-pass membrane protein				314
Q9TUA2 UniProt NPD GO	OR1E2_PANTR	Olfactory receptor 1E2	0.23	-	end	6 *	Membrane; multi-pass membrane protein				314
Q8NGR8 UniProt NPD GO	OR1L8_HUMAN	Olfactory receptor 1L8 (Olfactory receptor OR9-24)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				309
P58918 UniProt NPD GO	CXO6B_CONCT	Omega-conotoxin CVIB	0.23	-	nuc	0	Secreted protein				25
P37300 UniProt NPD GO	CXO7C_CONMA	Omega-conotoxin MVIIc precursor (SNX-230) (Fragment)	0.23	-	nuc	0	Secreted protein			1V4Q	29
P58915 UniProt NPD GO	CXO6A_CONTU	Omega-conotoxin TVIA (SNX-185)	0.23	-	mit	0	Secreted protein				26
P22080 UniProt NPD GO	ONCA_TAETA	Oncosphere antigen A (Fragment)	0.23	-	cyt	0					318
P18741 UniProt NPD GO	ZO15_XENLA	Oocyte zinc finger protein XLCOF15 (Fragment)	0.23	-	nuc	0	Nucleus (Potential)				140
P05035 UniProt NPD GO	PYRF_NEUCR	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.23	-	cyt	0					397
Q7Z8L4 UniProt NPD GO	PYRF_PENCA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.23	-	mit	0					276
Q6XJU9 UniProt NPD GO	OSTF1_MONAL	Osteoclast-stimulating factor 1 (Osteoclast-stimulating factor-like)	0.23	-	mit	0	Cytoplasm (By similarity)				214
P36718 UniProt NPD GO	OVGP1_PAPAN	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.23	-	cyt	0	Secretory granules				623
Q12889 UniProt NPD GO	OVGP1_HUMAN	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.23	-	cyt	0	Secretory granules		603578		678
Q8MIQ9 UniProt NPD GO	P_PIG	P protein (Melanocyte-specific transporter protein) (Pink-eyed dilution protein homolog)	0.23	-	end	12	Melanosome; melanosomal membrane; multi-pass membrane protein (By similarity)				845
Q9ERK9 UniProt NPD GO	P2RY6_MOUSE	P2Y purinoceptor 6 (P2Y6)	0.23	-	end	6 *	Membrane; multi-pass membrane protein				328
P22895 UniProt NPD GO	P34_SOYBN	P34 probable thiol protease precursor (EC 3.4.22.-)	0.23	-	exc	0	Vacuole. Protein storage vacuoles of seeds. This protein was wrongly thought to be associated with s ...				379
Q1JQD4 UniProt NPD GO	GIPC2_BOVIN	PDZ domain-containing protein GIPC2	0.23	-	nuc	0	Cytoplasm (Probable)				313
Q5RCI9 UniProt NPD GO	PCNP_PONPY	PEST proteolytic signal-containing nuclear protein (PEST-containing nuclear protein) (PCNP)	0.23	-	nuc	0	Nucleus (By similarity)				178
P23757 UniProt NPD GO	POXM_DROME	Paired box pox-meso protein (Paired box mesodermal protein)	0.23	-	nuc	0	Nucleus				402
P55166 UniProt NPD GO	PAX9_CHICK	Paired box protein Pax-9 (Fragment)	0.23	-	nuc	0	Nucleus				339
P42836 UniProt NPD GO	PFA3_YEAST	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.23	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane (sensu Fungi) [IDA]			336
Q59NR8 UniProt NPD GO	PFA5_CANAL	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.23	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				405
P15427 UniProt NPD GO	PAHO_RANCA	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.23	-	nuc	0	Secreted protein				36
O24210 UniProt NPD GO	PANC_ORYSA	Pantoate--beta-alanine ligase (EC 6.3.2.1) (Pantothenate synthetase) (Pantoate-activating enzyme)	0.23	-	mit	0	Cytoplasm (Potential)				313
P83326 UniProt NPD GO	PMEI_ACTCH	Pectinesterase inhibitor (Pectin methylesterase inhibitor) (PMEI)	0.23	-	nuc	0	Cytoplasm. Concentrated in a layer close to the cell membrane			1XG2	152
P62388 UniProt NPD GO	NXSA_PELPL	Pelamitoxin a	0.23	-	nuc	0	Secreted protein				60
P54152 UniProt NPD GO	MSRA_FRAAN	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.23	-	nuc	0					191
P53691 UniProt NPD GO	PPID_YEAST	Peptidyl-prolyl cis-trans isomerase CPR6 (EC 5.2.1.8) (PPIase) (Rotamase)	0.23	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			371
P92203 UniProt NPD GO	PER_DROEQ	Period circadian protein (Fragment)	0.23	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				395

You are viewing entries 47651 to 47700 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.