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
P48533 UniProt NPD GO	PTB2_XENLA	Pleiotrophic factor-beta-2 precursor (PTF-beta-2)	0.33	-	nuc	1 *	Secreted protein (By similarity)				161
Q2PCF1 UniProt NPD GO	PDR2_NICPL	Pleiotropic drug resistance protein 2 (NpPDR2)	0.33	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1461
P29468 UniProt NPD GO	PAP_YEAST	Poly(A) polymerase (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase)	0.33	-	cyt	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI] nucleoplasm [IPI]		1FA0	568
Q9UW26 UniProt NPD GO	PAPA_CANAL	Poly(A) polymerase PAPa (EC 2.7.7.19) (Polynucleotide adenylyltransferase a)	0.33	+	cyt	0	Nucleus (By similarity)				555
Q9BYE7 UniProt NPD GO	PCGF6_HUMAN	Polycomb group RING finger protein 6 (RING finger protein 134) (Mel18 and Bmi1-like RING finger)	0.33	-	cyt	0	Nucleus	PcG protein complex [TAS]	607816		352
O16023 UniProt NPD GO	ESC_MUSDO	Polycomb protein esc (Protein extra sex combs)	0.33	-	nuc	0	Nucleus (Probable)				428
Q08307 UniProt NPD GO	PPOE_LYCES	Polyphenol oxidase E, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.33	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				587
Q9MB14 UniProt NPD GO	PPO2_IPOBA	Polyphenol oxidase II, chloroplast precursor (EC 1.10.3.1) (PPO-II) (Catechol oxidase II)	0.33	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)				588
P28789 UniProt NPD GO	HEM3_YEAST	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.33	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			327
Q3LS21 UniProt NPD GO	KCNK9_MOUSE	Potassium channel subfamily K member 9 (Acid-sensitive potassium channel protein TASK-3) (TWIK-relat ...	0.33	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				402
P63141 UniProt NPD GO	KCNA2_MOUSE	Potassium voltage-gated channel subfamily A member 2 (Voltage-gated potassium channel subunit Kv1.2) ...	0.33	-	end	5	Membrane; multi-pass membrane protein				499
P63142 UniProt NPD GO	KCNA2_RAT	Potassium voltage-gated channel subfamily A member 2 (Voltage-gated potassium channel subunit Kv1.2) ...	0.33	-	end	5	Membrane; multi-pass membrane protein			2A79	499
P15384 UniProt NPD GO	KCNA3_RAT	Potassium voltage-gated channel subfamily A member 3 (Voltage-gated potassium channel subunit Kv1.3) ...	0.33	-	end	4	Membrane; multi-pass membrane protein				525
Q8WWG9 UniProt NPD GO	KCNE4_HUMAN	Potassium voltage-gated channel subfamily E member 4 (Minimum potassium ion channel-related peptide ...	0.33	-	nuc	1 *	Membrane; single-pass type I membrane protein		607775		170
Q4WLI5 UniProt NPD GO	RSE1_ASPFU	Pre-mRNA-splicing factor rse1	0.33	-	cyt	0	Nucleus (By similarity)				1225
Q9UTT2 UniProt NPD GO	RSE1_SCHPO	Pre-mRNA-splicing factor rse1 (Pre-mRNA-processing protein 12) (Spliceosome-associated protein 130)	0.33	-	cyt	0	Nucleus				1206
Q759E9 UniProt NPD GO	PAM17_ASHGO	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.33	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				186
P26196 UniProt NPD GO	DDX6_HUMAN	Probable ATP-dependent RNA helicase DDX6 (EC 3.6.1.-) (DEAD box protein 6) (ATP-dependent RNA helica ...	0.33	-	cyt	0	Cytoplasm. Processing bodies (PB)		600326	1VEC	483
Q9WVT0 UniProt NPD GO	GP116_RAT	Probable G-protein coupled receptor 116 precursor (G-protein coupled hepta-helical receptor Ig-hepta ...	0.33	-	end	7	Membrane; multi-pass membrane protein				1349
Q3UN16 UniProt NPD GO	GP162_MOUSE	Probable G-protein coupled receptor 162	0.33	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				588
Q8VWQ4 UniProt NPD GO	WRK56_ARATH	Probable WRKY transcription factor 56 (WRKY DNA-binding protein 56)	0.33	-	nuc	0	Nucleus (Probable)				195
Q9C6H5 UniProt NPD GO	WRK63_ARATH	Probable WRKY transcription factor 63 (WRKY DNA-binding protein 63)	0.33	-	nuc	0	Nucleus (Probable)				241
Q9FIJ7 UniProt NPD GO	KADC2_ARATH	Probable adenylate kinase 2, chloroplast precursor (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.33	-	mit	0	Plastid; chloroplast (By similarity)				283
Q9SVV6 UniProt NPD GO	KCO6_ARATH	Probable calcium-activated outward-rectifying potassium channel 6 (AtKCO6)	0.33	+	end	5	Membrane; multi-pass membrane protein				436
Q9V3D6 UniProt NPD GO	CPSF2_DROME	Probable cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.33	-	cyt	0	Nucleus (Potential)				756
Q8L7Z0 UniProt NPD GO	CNG17_ARATH	Probable cyclic nucleotide-gated ion channel 17 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.33	-	end	6	Cell membrane; multi-pass membrane protein (Potential)				720
Q8R089 UniProt NPD GO	FBSH_MOUSE	Probable fibrosin-1 long transcript protein	0.33	-	nuc	0					378
Q9VMA2 UniProt NPD GO	GALT_DROME	Probable galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP- ...	0.33	-	nuc	0					350
Q06915 UniProt NPD GO	EA6_ARATH	Probable glucan endo-1,3-beta-glucosidase A6 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrola ...	0.33	-	mit	0					478
P56521 UniProt NPD GO	HDAC_MAIZE	Probable histone deacetylase (RPD3 homolog)	0.33	-	cyt	0	Nucleus (By similarity)				513
Q4IBU5 UniProt NPD GO	SPC24_GIBZE	Probable kinetochore protein SPC24	0.33	-	cyt	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				201
Q5FVJ3 UniProt NPD GO	PPAC3_RAT	Probable lipid phosphate phosphatase PPAPDC3 (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 doma ...	0.33	-	end	4	Membrane; multi-pass membrane protein (Potential)				271
Q9N0Z4 UniProt NPD GO	AT11B_RABIT	Probable phospholipid-transporting ATPase IF (EC 3.6.3.1) (ATPase class I type 11B) (ATPase IR) (RIN ...	0.33	-	end	7	Membrane; multi-pass membrane protein. Isoform 2: Nucleus; nuclear inner membrane; multi-pass membra ...				1169
Q7PC80 UniProt NPD GO	PDR1_ORYSA	Probable pleiotropic drug resistance protein 1	0.33	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1468
Q4WVT3 UniProt NPD GO	MCH1_ASPFU	Probable transporter mch1	0.33	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				619
Q757L1 UniProt NPD GO	TREB_ASHGO	Probable trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.33	-	cyt	0					738
Q9VNL3 UniProt NPD GO	VATF2_DROME	Probable vacuolar ATP synthase subunit F 2 (EC 3.6.3.14) (V-ATPase F subunit 2) (Vacuolar proton pum ...	0.33	-	nuc	0					129
O60568 UniProt NPD GO	PLOD3_HUMAN	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor (EC 1.14.11.4) (Lysyl hydroxylase 3) (LH ...	0.33	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...	endoplasmic reticulum [TAS]	603066		738
Q5R6K5 UniProt NPD GO	PLOD3_PONPY	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor (EC 1.14.11.4) (Lysyl hydroxylase 3) (LH ...	0.33	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				738
P01238 UniProt NPD GO	PRL_PIG	Prolactin precursor (PRL)	0.33	-	exc	0	Secreted protein				229
Q5ZMB7 UniProt NPD GO	PNRC2_CHICK	Proline-rich nuclear receptor coactivator 2	0.33	-	nuc	0	Nucleus (Potential)				141
Q16647 UniProt NPD GO	PTGIS_HUMAN	Prostacyclin synthase (EC 5.3.99.4) (Prostaglandin I2 synthase)	0.33	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein		601699		500
P34995 UniProt NPD GO	PE2R1_HUMAN	Prostaglandin E2 receptor, EP1 subtype (Prostanoid EP1 receptor) (PGE receptor, EP1 subtype)	0.33	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	176802		402
P43115 UniProt NPD GO	PE2R3_HUMAN	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype) (PGE2-R ...	0.33	+	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] nuclear envelope [TAS] plasma membrane [TAS]	176806		390
P20366 UniProt NPD GO	TKN1_HUMAN	Protachykinin 1 precursor (PPT) [Contains: Substance P; Neurokinin A (NKA) (Substance K) (Neuromedin ...	0.33	-	exc	0	Secreted protein	extracellular space [TAS]	162320		129
P32196 UniProt NPD GO	PG3_PIG	Protegrin-3 precursor (PG-3)	0.33	-	mit	1 *	Secreted protein			1PFP	149
P32317 UniProt NPD GO	AFG1_YEAST	Protein AFG1	0.33	-	mit	0		mitochondrion [IDA]			509
Q9H5F2 UniProt NPD GO	CK001_HUMAN	Protein C11orf1	0.33	-	nuc	0	Nucleus	nucleus [NAS]			150
Q9BTA0 UniProt NPD GO	CA090_HUMAN	Protein C1orf90	0.33	-	mit	0					74
Q9NWU2 UniProt NPD GO	CT011_HUMAN	Protein C20orf11 (Two-hybrid associated protein 1 with RanBPM) (Twa1)	0.33	-	cyt	0	Nucleus				228

You are viewing entries 37851 to 37900 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.