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
Q3SYZ8 UniProt NPD GO	PDLI3_BOVIN	PDZ and LIM domain protein 3	0.18	-	nuc	0	Localizes to myofiber Z-lines (By similarity)				316
Q6GLJ6 UniProt NPD GO	PDLI3_XENLA	PDZ and LIM domain protein 3	0.18	-	nuc	0	Localizes to myofiber Z-lines (By similarity)				358
Q6QGC0 UniProt NPD GO	PDLI3_PIG	PDZ and LIM domain protein 3 (Actinin-associated LIM protein) (Alpha-actinin-2-associated LIM protei ...	0.18	-	nuc	0	Localizes to myofiber Z-lines (By similarity)				365
O81488 UniProt NPD GO	Y5621_ARATH	PHD finger protein At5g26210	0.18	-	nuc	1				1WE9	255
Q28466 UniProt NPD GO	PO2F1_MACEU	POU domain, class 2, transcription factor 1 (Octamer-binding transcription factor 1) (Oct-1) (OTF-1) ...	0.18	-	exc	0	Nucleus				75
Q6C4W5 UniProt NPD GO	PFA3_YARLI	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.18	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				401
Q4WN54 UniProt NPD GO	SWF1_ASPFU	Palmitoyltransferase swf1 (EC 2.3.1.-)	0.18	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				379
P06304 UniProt NPD GO	PAHO_ANSAN	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.18	-	nuc	0	Secreted protein				36
P41519 UniProt NPD GO	PAHO_CHIBR	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.18	-	nuc	0	Secreted protein				36
P68010 UniProt NPD GO	PAHO_EQUPR	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.18	-	nuc	0	Secreted protein				36
P68009 UniProt NPD GO	PAHO_EQUZE	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.18	-	nuc	0	Secreted protein				36
P33684 UniProt NPD GO	PAHO_MACMU	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.18	-	nuc	0	Secreted protein				36
P51694 UniProt NPD GO	PYY_BOVIN	Peptide YY precursor (PYY) (Peptide tyrosine tyrosine)	0.18	-	exc	0	Secreted protein				97
Q9Y7F7 UniProt NPD GO	PLMP_ARMME	Peptidyl-Lys metalloendopeptidase precursor (EC 3.4.24.20) (MEP) (AmMEP)	0.18	-	exc	0	Secreted protein. Binds strongly to beta-1,3-glucan and chitin, major polysaccharides constituting t ...				351
P52012 UniProt NPD GO	CYP4_CAEEL	Peptidyl-prolyl cis-trans isomerase 4 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-4) (Cyclophilin ...	0.18	-	cyt	0					523
Q26231 UniProt NPD GO	PER_RHACO	Period circadian protein (Fragment)	0.18	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				109
P52204 UniProt NPD GO	RDS_CANFA	Peripherin (Retinal degeneration slow protein)	0.18	-	end	3 *	Membrane; multi-pass membrane protein				346
P35906 UniProt NPD GO	RDS_FELCA	Peripherin (Retinal degeneration slow protein)	0.18	-	end	3 *	Membrane; multi-pass membrane protein				346
O42583 UniProt NPD GO	RDS_XENLA	Peripherin (Retinal degeneration slow protein) (xRDS38)	0.18	-	end	3 *	Membrane; multi-pass membrane protein				346
Q9SB81 UniProt NPD GO	PER42_ARATH	Peroxidase 42 precursor (EC 1.11.1.7) (Atperox P42) (PRXR1) (ATP1a/ATP1b)	0.18	-	exc	0	Secreted protein (By similarity)				330
Q9UKG9 UniProt NPD GO	OCTC_HUMAN	Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) (COT)	0.18	-	cyt	0	Peroxisome (Potential)	peroxisome [TAS]	606090		612
P23204 UniProt NPD GO	PPARA_MOUSE	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.18	+	cyt	0	Nucleus	nucleus [TAS]			468
Q92275 UniProt NPD GO	BAR1_SCHCO	Pheromone B alpha 1 receptor	0.18	-	end	6 *	Membrane; multi-pass membrane protein				639
P43511 UniProt NPD GO	PBAN_LYMDI	Pheromone biosynthesis-activating neuropeptide (Lyd-PBAN)	0.18	-	nuc	0	Secreted protein				33
Q78Y63 UniProt NPD GO	PDCL2_MOUSE	Phosducin-like protein 2	0.18	-	cyt	0					240
O04928 UniProt NPD GO	CDS1_ARATH	Phosphatidate cytidylyltransferase (EC 2.7.7.41) (CDP-diglyceride synthetase) (CDP-diglyceride pyrop ...	0.18	-	end	7	Membrane; multi-pass membrane protein (Potential)				421
O08888 UniProt NPD GO	PTSS2_CRIGR	Phosphatidylserine synthase 2 (EC 2.7.8.-) (PtdSer synthase 2) (PSS-2) (Serine-exchange enzyme II)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				474
Q9Z1X2 UniProt NPD GO	PTSS2_MOUSE	Phosphatidylserine synthase 2 (EC 2.7.8.-) (PtdSer synthase 2) (PSS-2) (Serine-exchange enzyme II)	0.18	-	end	7 *	Membrane; multi-pass membrane protein	intracellular [IDA]			473
Q7TSV4 UniProt NPD GO	PGM2_MOUSE	Phosphoglucomutase-2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2)	0.18	-	cyt	0	Cytoplasm (By similarity)				620
P54319 UniProt NPD GO	PLAP_RAT	Phospholipase A-2-activating protein (PLAP)	0.18	-	cyt	0					795
P00610 UniProt NPD GO	PA2_ENHSC	Phospholipase A2 (EC 3.1.1.4) (Myotoxin) (Toxin VI:5) (Phosphatidylcholine 2-acylhydrolase)	0.18	-	nuc	0	Secreted protein				119
P00609 UniProt NPD GO	PA23_NOTSC	Phospholipase A2 (EC 3.1.1.4) (Notechis II-5) (Phosphatidylcholine 2-acylhydrolase)	0.18	-	nuc	0	Secreted protein			2NOT	119
Q8UUH7 UniProt NPD GO	PA26_LATCO	Phospholipase A2 PC20 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.18	-	exc	0	Secreted protein (By similarity)				154
Q9PUH6 UniProt NPD GO	PA28_AUSSU	Phospholipase A2 isozyme S10-58F precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA ...	0.18	-	exc	0	Secreted protein (By similarity)				145
Q9PTA7 UniProt NPD GO	PA2B_BUNMU	Phospholipase A2, beta bungarotoxin A-AL2 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhy ...	0.18	-	nuc	0	Secreted protein (By similarity)				133
P14423 UniProt NPD GO	PA2GA_RAT	Phospholipase A2, membrane associated precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) ( ...	0.18	-	exc	1 *	Membrane; peripheral membrane protein				146
Q9T053 UniProt NPD GO	PLDG1_ARATH	Phospholipase D gamma 1 (EC 3.1.4.4) (AtPLDgamma1) (PLD gamma 1) (Choline phosphatase) (Lipophosphod ...	0.18	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Found mainly associated with intracellular membran ...				858
O15162 UniProt NPD GO	PLS1_HUMAN	Phospholipid scramblase 1 (PL scramblase 1) (Ca(2+)-dependent phospholipid scramblase 1) (Erythrocyt ...	0.18	-	nuc	0	Membrane; single-pass type II membrane protein	plasma membrane [TAS]	604170	1Y2A	318
O15305 UniProt NPD GO	PMM2_HUMAN	Phosphomannomutase 2 (EC 5.4.2.8) (PMM 2)	0.18	-	cyt	0	Cytoplasm		212065	2AMY	246
Q8BZB2 UniProt NPD GO	COAC_MOUSE	Phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) (PPC-DC) (CoaC)	0.18	-	cyt	0					204
O60256 UniProt NPD GO	KPRB_HUMAN	Phosphoribosyl pyrophosphate synthetase-associated protein 2 (PRPP synthetase-associated protein 2) ...	0.18	-	cyt	0			603762		369
Q8R574 UniProt NPD GO	KPRB_MOUSE	Phosphoribosyl pyrophosphate synthetase-associated protein 2 (PRPP synthetase-associated protein 2) ...	0.18	-	cyt	0					369
P51486 UniProt NPD GO	ARR1_CALVI	Phosrestin-2 (Phosrestin II) (Arrestin A) (Arrestin-1)	0.18	-	mit	0					363
Q9TM42 UniProt NPD GO	YCF3_CYACA	Photosystem I assembly protein ycf3	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				173
P49525 UniProt NPD GO	YCF3_ODOSI	Photosystem I assembly protein ycf3	0.18	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				179
Q9GDV1 UniProt NPD GO	YCF4_CARCL	Photosystem I assembly protein ycf4	0.18	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P32869 UniProt NPD GO	PSAD_CUCSA	Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI- ...	0.18	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...				207
P42048 UniProt NPD GO	PSAF_CUCSA	Photosystem I reaction center subunit III (Photosystem I 18.5 kDa protein) (PSI-F) (PS I subunit 7) ...	0.18	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				26
P13352 UniProt NPD GO	PSAH_CHLRE	Photosystem I reaction center subunit VI, chloroplast precursor (PSI-H) (Light-harvesting complex I ...	0.18	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				130
P05700 UniProt NPD GO	PSBC_EUGGR	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.18	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				461

You are viewing entries 53401 to 53450 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.