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
Q9UH03 UniProt NPD GO	SEPT3_HUMAN	Neuronal-specific septin-3	0.33	-	cyt	0			608314		345
Q6RUW3 UniProt NPD GO	NEUY_BOVIN	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.33	-	exc	1 *	Secreted protein				97
P57774 UniProt NPD GO	NEUY_MOUSE	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.33	-	exc	1 *	Secreted protein				97
P07808 UniProt NPD GO	NEUY_RAT	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.33	-	exc	1 *	Secreted protein				98
P14765 UniProt NPD GO	NEUY_SHEEP	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.33	-	exc	1 *	Secreted protein				97
P01304 UniProt NPD GO	NEUY_PIG	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.33	-	nuc	0	Secreted protein			1TZ5	76
Q61212 UniProt NPD GO	NPY6R_MOUSE	Neuropeptide Y receptor type 6 (NPY6-R) (Pancreatic polypeptide receptor 2) (PP2)	0.33	-	end	7 *	Membrane; multi-pass membrane protein				371
O46660 UniProt NPD GO	NOS2_MACMU	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.33	-	nuc	0					162
P09602 UniProt NPD GO	HMGN2_MOUSE	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.33	+	nuc	0	Nucleus				89
O35291 UniProt NPD GO	RNAS2_MOUSE	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Eosinophil cationic-type ribonuclease 4) (MR-4) ( ...	0.33	-	nuc	1 *	Lysosome (Probable). Matrix of eosinophil's large specific granule				155
O02279 UniProt NPD GO	NHR62_CAEEL	Nuclear hormone receptor family member nhr-62	0.33	-	mit	0	Nucleus (Potential)				515
Q23489 UniProt NPD GO	NHR9_CAEEL	Nuclear hormone receptor family member nhr-9	0.33	-	mit	0	Nucleus (Potential)				332
Q62227 UniProt NPD GO	SHP_MOUSE	Nuclear receptor 0B2 (Orphan nuclear receptor SHP) (Small heterodimer partner)	0.33	-	mit	0	Nucleus			1YMT	260
Q60EQ4 UniProt NPD GO	NFYB3_ORYSA	Nuclear transcription factor Y subunit B-3 (OsNF-YB-3) (Transcriptional activator HAP3B)	0.33	-	nuc	0	Nucleus (Probable)				185
Q58CM8 UniProt NPD GO	NFYCA_ARATH	Nuclear transcription factor Y subunit C-10 (AtNF-YC-10)	0.33	-	nuc	0	Nucleus (By similarity)				195
Q92791 UniProt NPD GO	NO55_HUMAN	Nucleolar autoantigen No55	0.33	-	exc	0	Nucleus; nucleolus. Localized uniformly throughout the granular component of the nucleolus and on th ...	nucleolus [TAS] synaptonemal complex [TAS]			437
P08199 UniProt NPD GO	NUCL_MESAU	Nucleolin (Protein C23)	0.33	+	nuc	0	Nucleus; nucleolus			1RKJ	713
Q5ZI22 UniProt NPD GO	NUPL2_CHICK	Nucleoporin-like 2	0.33	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By similarity)				413
Q8R1N4 UniProt NPD GO	NUDC3_MOUSE	NudC domain-containing protein 3	0.33	-	cyt	0					363
Q26350 UniProt NPD GO	CXO7D_CONMA	Omega-conotoxin MVIId precursor (SNX-238) (Fragment)	0.33	-	mit	0	Secreted protein				29
Q7ZT98 UniProt NPD GO	CRVP_OPHHA	Ophanin precursor (Opharin)	0.33	-	nuc	0	Secreted protein				239
Q96P65 UniProt NPD GO	QRFPR_HUMAN	Orexigenic neuropeptide QRFP receptor (G-protein coupled receptor 103) (SP9155) (AQ27)	0.33	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	606925		431
Q9TUP7 UniProt NPD GO	OX2R_CANFA	Orexin receptor type 2 (Ox2r) (Hypocretin receptor type 2)	0.33	-	end	7	Membrane; multi-pass membrane protein				444
O43614 UniProt NPD GO	OX2R_HUMAN	Orexin receptor type 2 (Ox2r) (Hypocretin receptor type 2)	0.33	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602393		444
P58308 UniProt NPD GO	OX2R_MOUSE	Orexin receptor type 2 (Ox2r) (Hypocretin receptor type 2)	0.33	-	end	7	Membrane; multi-pass membrane protein				460
Q9YI98 UniProt NPD GO	OAZ1_BRARE	Ornithine decarboxylase antizyme 1 (ODC antizyme, short form) (ODC-Az-S)	0.33	-	nuc	0					214
P10923 UniProt NPD GO	OSTP_MOUSE	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1) (Minopontin) (Early ...	0.33	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [ISS] extracellular region [NAS]			294
Q09180 UniProt NPD GO	MAP2_SCHPO	P-factor precursor	0.33	-	exc	0	Secreted protein				201
Q9CQX4 UniProt NPD GO	PAF_MOUSE	PCNA-associated factor (p15PAF) (HCV NS5A-transactivated protein 9 homolog)	0.33	-	mit	0	Nucleus (By similarity). Mitochondrion (By similarity)				110
Q9JMD3 UniProt NPD GO	PCTL_MOUSE	PCTP-like protein (PCTP-L) (StAR-related lipid transfer protein 10) (StARD10) (START domain-containi ...	0.33	-	nuc	0	Flagellum. In testis was predominantly detected at the flagella of elongated spermatids, with a stro ...				291
P36202 UniProt NPD GO	PDLI4_RAT	PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein) (RIT-18) (H-REV18)	0.33	-	nuc	0					330
Q9Z1Z9 UniProt NPD GO	PDLI7_RAT	PDZ and LIM domain protein 7 (LIM mineralization protein) (LMP) (Protein enigma)	0.33	-	nuc	0	Cytoplasm (By similarity). Colocalizes with RET to the cell periphery and in some cytoskeletal compo ...				457
Q9BQY4 UniProt NPD GO	PEPP2_HUMAN	Paired-like homeobox protein PEPP-2 (Testis homeobox gene 1)	0.33	+	cyt	0	Nucleus (By similarity)		300447		288
Q6BMV2 UniProt NPD GO	PFA3_DEBHA	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.33	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				405
P25291 UniProt NPD GO	GP2_CANFA	Pancreatic secretory granule membrane major glycoprotein GP2 precursor (Pancreatic zymogen granule m ...	0.33	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein. Secreted after cleavage in the pancreatic ...				509
Q9HBH1 UniProt NPD GO	DEFM_HUMAN	Peptide deformylase, mitochondrial precursor (EC 3.5.1.88) (Polypeptide deformylase)	0.33	-	mit	0	Mitochondrion (Potential)	mitochondrion [IDA]			243
P47103 UniProt NPD GO	CYP7_YEAST	Peptidyl-prolyl cis-trans isomerase CYP7 (EC 5.2.1.8) (PPIase) (Rotamase)	0.33	-	cyt	0		cytosol [IPI]			393
Q25020 UniProt NPD GO	PER_HYACE	Period circadian protein (Fragment)	0.33	-	cyt	0	Nucleus. Nuclear at specific periods of the day. Interaction with TIM is required for nuclear locali ...				358
P25635 UniProt NPD GO	PWP2_YEAST	Periodic tryptophan protein 2 (U3 small nucleolar RNA-associated protein 1) (U3 snoRNA-associated pr ...	0.33	-	cyt	0	Nucleus; nucleolus	90S preribosome [IDA] cytoplasm [IDA] small nucleolar ribonucleoprotein complex [IPI]			923
Q9SD46 UniProt NPD GO	PER36_ARATH	Peroxidase 36 precursor (EC 1.11.1.7) (Atperox P36)	0.33	-	nuc	0	Secreted protein (By similarity)				336
Q9FL16 UniProt NPD GO	PER63_ARATH	Peroxidase 63 precursor (EC 1.11.1.7) (Atperox P63) (ATP26a)	0.33	-	exc	0	Secreted protein (By similarity)				328
Q8VCI5 UniProt NPD GO	PEX19_MOUSE	Peroxisomal biogenesis factor 19 (Peroxin-19) (Peroxisomal farnesylated protein) (PxF)	0.33	-	nuc	0	Cytoplasm (By similarity). Mainly (By similarity). Peroxisome; peroxisomal membrane; lipid-anchor; c ...				299
Q9Z211 UniProt NPD GO	PX11A_MOUSE	Peroxisomal membrane protein 11A (Peroxin-11A) (Peroxisomal biogenesis factor 11A) (PEX11alpha)	0.33	-	cyt	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				246
P15625 UniProt NPD GO	SYFA_YEAST	Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase alpha chain) (Phe ...	0.33	-	nuc	0	Cytoplasm	cytoplasm [IDA] phenylalanine-tRNA ligase complex [TAS]			502
P20584 UniProt NPD GO	PPA1_ASPNG	Phosphate-repressible acid phosphatase precursor (EC 3.1.3.2) (Acid phosphatase PII)	0.33	-	exc	0					436
Q9SCY0 UniProt NPD GO	PGMP_ARATH	Phosphoglucomutase, chloroplast precursor (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.33	-	mit	0	Plastid; chloroplast				623
P31325 UniProt NPD GO	PHKG2_RAT	Phosphorylase b kinase gamma catalytic chain, testis/liver isoform (EC 2.7.11.19) (PHK-gamma-T) (Pho ...	0.33	-	cyt	0					406
Q9QUL0 UniProt NPD GO	PRLPI_RAT	Placental prolactin-like protein I precursor (PRL-like protein I) (PLP-I) (Decidualin) (Prolactin-li ...	0.33	-	nuc	1 *	Secreted protein (By similarity)				211
P12545 UniProt NPD GO	PLMN_MACMU	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Plasmin he ...	0.33	-	nuc	0	Secreted protein				810
Q08481 UniProt NPD GO	PECA1_MOUSE	Platelet endothelial cell adhesion molecule precursor (PECAM-1) (CD31 antigen)	0.33	-	exc	1	Membrane; single-pass type I membrane protein	lipid raft [IDA] plasma membrane [IDA]			727

You are viewing entries 37801 to 37850 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.