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
Q8NG92 UniProt NPD GO	O13H1_HUMAN	Olfactory receptor 13H1	0.16	-	end	7 *	Membrane; multi-pass membrane protein				308
Q8NGT7 UniProt NPD GO	O2A12_HUMAN	Olfactory receptor 2A12	0.16	-	end	7 *	Membrane; multi-pass membrane protein				310
Q8NGM9 UniProt NPD GO	OR8D4_HUMAN	Olfactory receptor 8D4	0.16	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NH09 UniProt NPD GO	OR8S1_HUMAN	Olfactory receptor 8S1	0.16	-	end	5 *	Membrane; multi-pass membrane protein				359
Q9XYZ1 UniProt NPD GO	CXO2A_CONPL	Omega-conotoxin PuIIA precursor	0.16	-	exc	1 *	Secreted protein (By similarity)				74
Q9VCA2 UniProt NPD GO	ORCT_DROME	Organic cation transporter protein	0.16	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			548
P40148 UniProt NPD GO	OSTC_SPAAU	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.16	-	exc	0	Secreted protein				97
Q08952 UniProt NPD GO	OXR1_YEAST	Oxidation resistance protein 1	0.16	-	nuc	0	Mitochondrion	mitochondrion [IDA]			273
P70536 UniProt NPD GO	OXYR_RAT	Oxytocin receptor (OT-R)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				388
P56278 UniProt NPD GO	MTCPB_HUMAN	P13 MTCP-1 protein (Mature T-cell proliferation-1 type B1) (MTCP-1 type B1) (P13MTCP1)	0.16	-	nuc	0			300116	1QTU	107
P49653 UniProt NPD GO	P2RX2_RAT	P2X purinoceptor 2 (ATP receptor) (P2X2) (Purinergic receptor)	0.16	-	mit	1 *	Membrane; multi-pass membrane protein				472
Q8TF64 UniProt NPD GO	GIPC3_HUMAN	PDZ domain-containing protein GIPC3	0.16	-	mit	0			608792		312
Q9H4Q4 UniProt NPD GO	PRD12_HUMAN	PR domain zinc finger protein 12 (PR domain-containing protein 12)	0.16	-	cyt	0	Nucleus (Potential)				367
Q6BHT4 UniProt NPD GO	ERFB_DEBHA	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.16	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				371
Q7RWM9 UniProt NPD GO	SWF1_NEUCR	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.16	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				429
Q9Y397 UniProt NPD GO	ZDHC9_HUMAN	Palmitoyltransferase ZDHHC9 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 9) (DHHC-9) (DH ...	0.16	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				364
O80722 UniProt NPD GO	PME4_ARATH	Pectinesterase-4 precursor (EC 3.1.1.11) (Pectin methylesterase 4) (PE 4) (VANGUARD1-like protein 1) ...	0.16	-	end	1 *					588
Q9LNF2 UniProt NPD GO	PMEI1_ARATH	Pectinmethylesterase inhibitor 1 precursor (AtPMEI1)	0.16	-	exc	1 *				1X91	176
Q9N2D4 UniProt NPD GO	PEPA_CALJA	Pepsin A precursor (EC 3.4.23.1)	0.16	-	exc	0	Secreted protein				387
P11489 UniProt NPD GO	PEPA_MACMU	Pepsin A precursor (EC 3.4.23.1)	0.16	-	exc	0	Secreted protein				388
P27821 UniProt NPD GO	PEPA2_RABIT	Pepsin II-2/3 precursor (EC 3.4.23.1) (Pepsin A)	0.16	-	exc	0	Secreted protein				387
P28713 UniProt NPD GO	PEPA4_RABIT	Pepsin II-4 precursor (EC 3.4.23.1) (Pepsin A)	0.16	-	exc	0	Secreted protein				387
P69094 UniProt NPD GO	PYY_LEPSP	Peptide YY-like (PYY) (Neuropeptide Y-related peptide)	0.16	-	nuc	0	Secreted protein				36
P69095 UniProt NPD GO	PYY_SCYCA	Peptide YY-like (PYY) (Neuropeptide Y-related peptide)	0.16	-	nuc	0	Secreted protein				36
P69096 UniProt NPD GO	PYY_SQUAC	Peptide YY-like (PYY) (Neuropeptide Y-related peptide)	0.16	-	nuc	0	Secreted protein				36
P48098 UniProt NPD GO	PYY_LAMFL	Peptide YY-like precursor (PYY)	0.16	-	exc	1 *	Secreted protein				93
Q8SPP7 UniProt NPD GO	PGRP_BOVIN	Peptidoglycan recognition protein precursor (Peptidoglycan recognition protein short) (PGRP-S) (Olig ...	0.16	-	exc	0	Secreted protein; cytoplasmic granule				190
P15499 UniProt NPD GO	RDS_MOUSE	Peripherin (Retinal degeneration slow protein)	0.16	-	end	3 *	Membrane; multi-pass membrane protein				346
P17438 UniProt NPD GO	RDS_RAT	Peripherin (Retinal degeneration slow protein)	0.16	-	end	3 *	Membrane; multi-pass membrane protein				346
P16147 UniProt NPD GO	PERX_LUPPO	Peroxidase (EC 1.11.1.7) (Fragment)	0.16	-	nuc	0					158
P27337 UniProt NPD GO	PER1_HORVU	Peroxidase 1 precursor (EC 1.11.1.7)	0.16	-	exc	0	Secreted protein (By similarity)				315
Q42580 UniProt NPD GO	PER21_ARATH	Peroxidase 21 precursor (EC 1.11.1.7) (Atperox P21) (PRXR5) (ATP2a/ATP2b)	0.16	-	exc	1 *					327
O81772 UniProt NPD GO	PER46_ARATH	Peroxidase 46 precursor (EC 1.11.1.7) (Atperox P46) (ATP48)	0.16	-	exc	1 *	Secreted protein (By similarity)				326
Q9FG34 UniProt NPD GO	PER54_ARATH	Peroxidase 54 precursor (EC 1.11.1.7) (Atperox P54) (ATP29a)	0.16	-	nuc	1 *	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				358
Q8X182 UniProt NPD GO	CAT2_NEUCR	Peroxidase/catalase 2 (EC 1.11.1.6) (Catalase-peroxidase)	0.16	-	cyt	0					753
Q9GLW7 UniProt NPD GO	PRDX5_CERAE	Peroxiredoxin-5, mitochondrial precursor (EC 1.11.1.15) (Prx-V) (Thioredoxin reductase)	0.16	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity). Peroxisome (By similarity)				215
Q9GLW9 UniProt NPD GO	PRDX5_PAPHA	Peroxiredoxin-5, mitochondrial precursor (EC 1.11.1.15) (Prx-V) (Thioredoxin reductase)	0.16	-	cyt	0	Mitochondrion (By similarity). Cytoplasm (By similarity). Peroxisome (By similarity)				215
Q9BQG2 UniProt NPD GO	NUD12_HUMAN	Peroxisomal NADH pyrophosphatase NUDT12 (EC 3.6.1.22) (Nucleoside diphosphate-linked moiety X motif ...	0.16	-	cyt	0	Peroxisome		609232		462
Q99155 UniProt NPD GO	PEX2_YARLI	Peroxisomal biogenesis factor 2 (Peroxin-2) (Peroxisomal protein PAY5)	0.16	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (Potential)				381
P97852 UniProt NPD GO	DHB4_RAT	Peroxisomal multifunctional enzyme type 2 (MFE-2) (D-bifunctional protein) (DBP) (17-beta-hydroxyste ...	0.16	-	pox	0	Peroxisome (By similarity)			1GZ6	734
O70301 UniProt NPD GO	PSPN_RAT	Persephin precursor (PSP)	0.16	-	exc	0	Secreted protein				156
Q42858 UniProt NPD GO	PAL2_IPOBA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.16	-	nuc	0	Cytoplasm (Probable)				708
O23924 UniProt NPD GO	PALY_DIGLA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.16	-	nuc	0	Cytoplasm (Probable)				713
P27990 UniProt NPD GO	PALY_MEDSA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.16	-	nuc	0	Cytoplasm (Probable)				725
Q9SMK9 UniProt NPD GO	PAL2_CICAR	Phenylalanine ammonia-lyase 2 (EC 4.3.1.5)	0.16	-	nuc	0	Cytoplasm (Probable)				718
P45731 UniProt NPD GO	PAL1_POPKI	Phenylalanine ammonia-lyase G1 (EC 4.3.1.5)	0.16	-	nuc	0	Cytoplasm (Probable)				682
P07218 UniProt NPD GO	PAL1_PHAVU	Phenylalanine ammonia-lyase class 1 (EC 4.3.1.5) (Phenylalanine ammonia-lyase class I) (Fragment)	0.16	-	nuc	0	Cytoplasm (Probable)				506
P12384 UniProt NPD GO	STE2_SACKL	Pheromone alpha factor receptor	0.16	-	end	7 *	Membrane; multi-pass membrane protein				426
P48739 UniProt NPD GO	PIPNB_HUMAN	Phosphatidylinositol transfer protein beta isoform (PtdIns transfer protein beta) (PtdInsTP) (PI-TP- ...	0.16	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus (By similarity)		606876		270
P27465 UniProt NPD GO	PISD_CRIGR	Phosphatidylserine decarboxylase proenzyme (EC 4.1.1.65) [Contains: Phosphatidylserine decarboxylase ...	0.16	-	mit	0	Mitochondrion				409

You are viewing entries 56001 to 56050 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.