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
O93474 UniProt NPD GO	NT7_CYPCA	Neurotrophin-7 precursor (NT-7) (Fragment)	0.11	-	cyt	0	Secreted protein				140
P60030 UniProt NPD GO	DEF1_MACMU	Neutrophil defensin 1 precursor (RMAD-1)	0.11	-	exc	0	Secreted protein				96
P81466 UniProt NPD GO	DEF2_MESAU	Neutrophil defensin 2 (HANP-2)	0.11	-	nuc	0	Secreted protein				31
Q96T66 UniProt NPD GO	NMNA3_HUMAN	Nicotinamide mononucleotide adenylyltransferase 3 (EC 2.7.7.1) (NMN adenylyltransferase 3)	0.11	-	cyt	0	Nucleus (Probable)		608702	1NUU	252
P49019 UniProt NPD GO	G109B_HUMAN	Nicotinic acid receptor 2 (G-protein coupled receptor 109B) (G-protein coupled receptor HM74) (G-pro ...	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606039		387
Q9UUB8 UniProt NPD GO	YH9J_SCHPO	NifU-like protein C1709.19c	0.11	-	mit	0					260
P27783 UniProt NPD GO	NIA_BETVE	Nitrate reductase [NAD(P)H] (EC 1.7.1.2) (NR)	0.11	-	nuc	0					898
P23762 UniProt NPD GO	NMR_NEUCR	Nitrogen metabolic regulation protein (Protein NMR)	0.11	-	cyt	0	Nucleus (Potential)				488
P08863 UniProt NPD GO	NO26B_SOYBN	Nodulin 26B precursor (N-26B)	0.11	-	exc	0					219
P52299 UniProt NPD GO	NCBP2_XENLA	Nuclear cap-binding protein subunit 2 (20 kDa nuclear cap-binding protein) (NCBP 20 kDa subunit) (CB ...	0.11	-	cyt	0	Nucleus	nucleus [ISS]			148
P87102 UniProt NPD GO	NTF2_NEUCR	Nuclear transport factor 2 (NTF-2)	0.11	-	cyt	0	Cytoplasm (By similarity)				124
O64903 UniProt NPD GO	NDK2_ARATH	Nucleoside diphosphate kinase II, chloroplast precursor (EC 2.7.4.6) (NDK II) (NDP kinase II) (NDPK ...	0.11	-	mit	0	Plastid; chloroplast (Potential)			1S59	231
Q27893 UniProt NPD GO	NTP1_TOXGO	Nucleoside-triphosphatase 1 precursor (EC 3.6.1.15) (Nucleoside-triphosphatase I) (NTPase-I) (Nucleo ...	0.11	-	nuc	0	Secreted protein. Found in host cell parasitophorous vacuole				628
Q99158 UniProt NPD GO	SIL1_YARLI	Nucleotide exchange factor SIL1 precursor (Protein SLS1)	0.11	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen				426
P29525 UniProt NPD GO	OLEO1_ARATH	Oleosin 18.5 kDa	0.11	-	end	2	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				173
Q8VFK2 UniProt NPD GO	O1002_MOUSE	Olfactory receptor 1002 (Olfactory receptor 175-2)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				318
Q8VGS1 UniProt NPD GO	O1038_MOUSE	Olfactory receptor 1038 (Olfactory receptor 185-3)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				319
Q8VGR9 UniProt NPD GO	O1044_MOUSE	Olfactory receptor 1044 (Olfactory receptor 185-4)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8VES2 UniProt NPD GO	O1102_MOUSE	Olfactory receptor 1102 (Olfactory receptor 179-4)	0.11	+	end	7 *	Membrane; multi-pass membrane protein				324
Q8NGV5 UniProt NPD GO	O13D1_HUMAN	Olfactory receptor 13D1	0.11	-	end	7 *	Membrane; multi-pass membrane protein				314
Q60880 UniProt NPD GO	OL141_MOUSE	Olfactory receptor 141 (Olfactory receptor 4B)	0.11	-	end	6 *	Membrane; multi-pass membrane protein				325
Q8NGU4 UniProt NPD GO	OR2I1_HUMAN	Olfactory receptor 2I1	0.11	-	end	5 *	Membrane; multi-pass membrane protein				316
Q8NGY9 UniProt NPD GO	OR2L8_HUMAN	Olfactory receptor 2L8 (Olfactory receptor OR1-46)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NG81 UniProt NPD GO	OR2M7_HUMAN	Olfactory receptor 2M7 (Olfactory receptor OR1-58)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGB4 UniProt NPD GO	OR4S1_HUMAN	Olfactory receptor 4S1	0.11	-	end	6 *	Membrane; multi-pass membrane protein				309
Q6IEU7 UniProt NPD GO	OR5MA_HUMAN	Olfactory receptor 5M10 (Olfactory receptor OR11-207)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				315
Q9UGF5 UniProt NPD GO	OR5U1_HUMAN	Olfactory receptor 5U1 (Hs6M1-28)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				321
Q96RD1 UniProt NPD GO	OR6C1_HUMAN	Olfactory receptor 6C1 (OST267)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				312
P23272 UniProt NPD GO	OLFI9_RAT	Olfactory receptor-like protein I9	0.11	-	end	6 *	Membrane; multi-pass membrane protein				314
P40897 UniProt NPD GO	OPT1_YEAST	Oligopeptide transporter 1	0.11	-	end	12	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [IDA] integral to plasma membrane [IMP]			799
P48627 UniProt NPD GO	FAD6C_BRANA	Omega-6 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.11	-	end	2	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				443
P48628 UniProt NPD GO	FAD6C_SOYBN	Omega-6 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.11	+	mit	4	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				424
P58919 UniProt NPD GO	CXO6C_CONCT	Omega-conotoxin CVIC	0.11	-	nuc	0	Secreted protein				26
P30842 UniProt NPD GO	CROM_OMMSL	Omega-crystallin	0.11	-	cyt	0					494
Q95R48 UniProt NPD GO	OCTL_DROME	Organic cation transporter-like protein	0.11	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			567
P11066 UniProt NPD GO	OTC_ASPNG	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix				370
P31317 UniProt NPD GO	OTC_SCHPO	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			327
P78599 UniProt NPD GO	DCOR_CANAL	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.11	-	nuc	0					473
Q9YI97 UniProt NPD GO	OAZ2_BRARE	Ornithine decarboxylase antizyme 2 (ODC antizyme, long form) (ODC-Az-L)	0.11	-	mit	0					218
P35788 UniProt NPD GO	PYRE_COLGR	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.11	-	cyt	0					233
P08309 UniProt NPD GO	PYRE_PODAN	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.11	-	cyt	0					231
Q96WP7 UniProt NPD GO	PYRF_ASPKA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.11	-	mit	0					277
P07817 UniProt NPD GO	PYRF_ASPNG	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.11	-	mit	0					277
P28296 UniProt NPD GO	ORYZ_ASPFU	Oryzin precursor (EC 3.4.21.63) (Alkaline proteinase) (ALP) (Elastase) (Elastinolytic serine protein ...	0.11	-	exc	0	Secreted protein				403
Q01591 UniProt NPD GO	TPM1_LYCES	Osmotin-like protein TPM-1 precursor (PR P23) (Fragment)	0.11	-	exc	0					238
Q28042 UniProt NPD GO	OVGP1_BOVIN	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.11	-	cyt	0	Secretory granules				537
Q9SLQ8 UniProt NPD GO	PSBP_CUCSA	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.11	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				263
Q41048 UniProt NPD GO	PSBQ1_MAIZE	Oxygen-evolving enhancer protein 3-1, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolvin ...	0.11	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				217
P56449 UniProt NPD GO	OXYR_BOVIN	Oxytocin receptor (OT-R)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				391
P32005 UniProt NPD GO	NEU1_PAPHA	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1] (Fragment)	0.11	-	nuc	0					85

You are viewing entries 63151 to 63200 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.