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
P12140 UniProt NPD GO	RK22_ORYSA	Chloroplast 50S ribosomal protein L22	0.51	-	nuc	0	Plastid; chloroplast				149
Q68RW7 UniProt NPD GO	RK22_PANGI	Chloroplast 50S ribosomal protein L22	0.51	-	mit	0	Plastid; chloroplast				160
P49562 UniProt NPD GO	RK29_ODOSI	Chloroplast 50S ribosomal protein L29	0.51	+	nuc	0	Plastid; chloroplast				89
Q8WI08 UniProt NPD GO	CEMA_PSINU	Chloroplast envelope membrane protein	0.51	-	nuc	5 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				449
Q6ZQ11 UniProt NPD GO	CHSS1_MOUSE	Chondroitin sulfate synthase 1 (EC 2.4.1.175) (Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-be ...	0.51	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				800
Q5KFF1 UniProt NPD GO	EAF3_CRYNE	Chromatin modification-related protein EAF3	0.51	-	cyt	0	Nucleus (By similarity)				305
Q6FJV4 UniProt NPD GO	EAF5_CANGA	Chromatin modification-related protein EAF5	0.51	-	nuc	0	Nucleus (By similarity)				205
P29742 UniProt NPD GO	CLH_DROME	Clathrin heavy chain	0.51	-	cyt	0	Cytoplasmic face of coated pits and vesicles	clathrin vesicle coat [TAS] coated pit [TAS] coated vesicle [TAS] synaptic vesicle [TAS]			1678
P08082 UniProt NPD GO	CLCB_RAT	Clathrin light chain B (Lcb)	0.51	-	nuc	0	Cytoplasmic face of coated pits and vesicles	clathrin coat of coated pit [NAS] clathrin vesicle coat [NAS]			229
Q15846 UniProt NPD GO	CLUL1_HUMAN	Clusterin-like protein 1 precursor (Retinal-specific clusterin-like protein)	0.51	-	cyt	0	Secreted protein (Probable)				466
Q07968 UniProt NPD GO	F13B_MOUSE	Coagulation factor XIII B chain precursor (Protein-glutamine gamma-glutamyltransferase B chain) (Tra ...	0.51	-	exc	0					668
Q6GLE1 UniProt NPD GO	CCD25_XENTR	Coiled-coil domain-containing protein 25	0.51	+	nuc	0					206
Q96A33 UniProt NPD GO	CCD47_HUMAN	Coiled-coil domain-containing protein 47 precursor	0.51	-	end	0	Membrane; single-pass membrane protein (Potential)				483
Q5RCI4 UniProt NPD GO	CCD47_PONPY	Coiled-coil domain-containing protein 47 precursor	0.51	-	end	0	Membrane; single-pass membrane protein (Potential)				483
Q2TBK4 UniProt NPD GO	CCDC5_BOVIN	Coiled-coil domain-containing protein 5	0.51	-	nuc	0	Cytoplasm (By similarity). Spindle (By similarity). Localizes with the spindle poles in mitotic cell ...				278
P20908 UniProt NPD GO	CO5A1_HUMAN	Collagen alpha-1(V) chain precursor	0.51	-	nuc	0		collagen type V [TAS]	120215	1A9A	1838
Q61245 UniProt NPD GO	COBA1_MOUSE	Collagen alpha-1(XI) chain precursor	0.51	-	nuc	0					1804
P25940 UniProt NPD GO	CO5A3_HUMAN	Collagen alpha-3(V) chain precursor	0.51	+	exc	0		collagen type V [TAS]	120216		1745
P02748 UniProt NPD GO	CO9_HUMAN	Complement component C9 precursor [Contains: Complement component C9a; Complement component C9b]	0.51	-	mit	0		integral to plasma membrane [TAS]	120940		559
P08603 UniProt NPD GO	CFAH_HUMAN	Complement factor H precursor (H factor 1)	0.51	-	mit	0	Secreted protein	extracellular space [TAS]	134370	2G7I	1231
P53951 UniProt NPD GO	COG5_YEAST	Conserved oligomeric Golgi complex subunit 5 (COG complex subunit 5) (Complexed with DOR1 protein 4) ...	0.51	-	nuc	0		Golgi transport complex [IPI]			403
Q5RD64 UniProt NPD GO	CNTP2_PONPY	Contactin-associated protein-like 2 precursor	0.51	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1331
P01190 UniProt NPD GO	COLI_BOVIN	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.51	-	nuc	0					265
P87090 UniProt NPD GO	CPC1_CRYPA	Cross-pathway control protein 1	0.51	-	nuc	0	Nucleus				247
P18832 UniProt NPD GO	COL7_CAEEL	Cuticle collagen 7 precursor	0.51	+	nuc	1 *					316
Q5MAI5 UniProt NPD GO	CDKL4_HUMAN	Cyclin-dependent kinase-like 4 (EC 2.7.11.22)	0.51	-	cyt	0	Cytoplasm (Probable)				315
O44220 UniProt NPD GO	C12B1_DROAC	Cytochrome P450 12b1, mitochondrial precursor (EC 1.14.-.-) (CYPXIIB1)	0.51	-	mit	0	Mitochondrion (Probable)				532
P51871 UniProt NPD GO	CP4F6_RAT	Cytochrome P450 4F6 (EC 1.14.14.1) (CYPIVF6)	0.51	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				537
P22680 UniProt NPD GO	CP7A1_HUMAN	Cytochrome P450 7A1 (Cholesterol 7-alpha-monooxygenase) (CYPVII) (EC 1.14.13.17) (Cholesterol 7-alph ...	0.51	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		118455		504
P16568 UniProt NPD GO	BICD_DROME	Cytoskeleton-like bicaudal D protein	0.51	-	nuc	0					782
P47712 UniProt NPD GO	PA24A_HUMAN	Cytosolic phospholipase A2 (cPLA2) (Phospholipase A2 group IVA) [Includes: Phospholipase A2 (EC 3.1. ...	0.51	-	cyt	0	Cytoplasm. Cytoplasmic vesicle. Translocates to membrane vesicles in a calcium-dependent fashion	cytosol [NAS] integral to membrane [NAS]	600522	1RLW	749
P47713 UniProt NPD GO	PA24A_MOUSE	Cytosolic phospholipase A2 (cPLA2) (Phospholipase A2 group IVA) [Includes: Phospholipase A2 (EC 3.1. ...	0.51	-	cyt	0	Cytoplasm. Cytoplasmic vesicle. Translocates to membrane vesicles in a calcium-dependent fashion				748
Q694B8 UniProt NPD GO	ABC3G_LAGLA	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.51	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				381
Q42572 UniProt NPD GO	DNLI_ARATH	DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])	0.51	-	mit	0	Nucleus (By similarity)				790
P90829 UniProt NPD GO	DPOD_CAEEL	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.51	-	cyt	0	Nucleus (By similarity)				1081
Q14566 UniProt NPD GO	MCM6_HUMAN	DNA replication licensing factor MCM6 (p105MCM)	0.51	-	cyt	0	Nucleus (By similarity)	nucleus [NAS]	601806		821
P48377 UniProt NPD GO	RFX1_MOUSE	DNA-binding protein RFX1	0.51	+	nuc	0	Nucleus (By similarity)				963
Q56P13 UniProt NPD GO	RPOB_LACSA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.51	-	cyt	0	Plastid; chloroplast				1060
Q6L3A7 UniProt NPD GO	RPOB_SACHY	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.51	-	nuc	0	Plastid; chloroplast				1075
Q63871 UniProt NPD GO	RPC10_MOUSE	DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide (EC 2.7.7.6) (ABC10-alpha) (RPB7.0) ...	0.51	-	nuc	0	Nucleus				58
Q12395 UniProt NPD GO	DCN1_YEAST	Defective in cullin neddylation protein 1	0.51	-	cyt	0					269
O93456 UniProt NPD GO	DEM_PACDA	Dermorphin precursor [Contains: [Ile2]-deltorphin; Dermorphin]	0.51	+	exc	0	Secreted protein	extracellular region [ISS]			201
P49621 UniProt NPD GO	DGKB_RAT	Diacylglycerol kinase beta (EC 2.7.1.107) (Diglyceride kinase beta) (DGK-beta) (DAG kinase beta) (90 ...	0.51	+	nuc	0	Cytoplasm. Membrane. Can be loosely bound to the membranes	membrane fraction [IDA]			801
Q5AZJ7 UniProt NPD GO	DPH1_EMENI	Diphthamide biosynthesis protein 1	0.51	-	cyt	0	Cytoplasm (By similarity)				431
O75553 UniProt NPD GO	DAB1_HUMAN	Disabled homolog 1	0.51	-	nuc	0			603448		555
P78352 UniProt NPD GO	DLG4_HUMAN	Discs large homolog 4 (Postsynaptic density protein 95) (PSD-95) (Synapse-associated protein 90) (SA ...	0.51	-	nuc	0	Cell membrane; peripheral membrane protein. High levels in postsynaptic density of neurons in the fo ...	cortical cytoskeleton [IDA] postsynaptic membrane [IDA]	602887	1KEF	724
Q62108 UniProt NPD GO	DLG4_MOUSE	Discs large homolog 4 (Postsynaptic density protein 95) (PSD-95) (Synapse-associated protein 90) (SA ...	0.51	-	nuc	0	Membrane-associated. High levels in postsynaptic density of neurons in the forebrain. Also in presyn ...	cytoplasm [NAS] extrinsic to internal side of plasma membrane [IDA] membrane fraction [IDA] synapse [IDA]			724
Q8W4J9 UniProt NPD GO	RPP8_ARATH	Disease resistance protein RPP8 (Resistance to Peronospora parasitica protein 8)	0.51	-	cyt	0					908
Q9N287 UniProt NPD GO	DJC12_BOVIN	DnaJ homolog subfamily C member 12 (J domain-containing protein 1)	0.51	-	nuc	0					198
Q5RCM7 UniProt NPD GO	DJC16_PONPY	DnaJ homolog subfamily C member 16 precursor	0.51	-	end	1 *	Membrane; single-pass type IV membrane protein (Potential)				782

You are viewing entries 24251 to 24300 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.