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
Q4FAT7 UniProt NPD GO	BGLR_PIG	Beta-glucuronidase precursor (EC 3.2.1.31)	0.25	-	mit	1 *	Lysosome (By similarity)				652
P33685 UniProt NPD GO	LACB1_CANFA	Beta-lactoglobulin-1 (Beta-LG-1) (Beta-lactoglobulin I)	0.25	-	cyt	0	Secreted protein				161
P33688 UniProt NPD GO	LACB3_FELCA	Beta-lactoglobulin-3 (Beta-LG-3) (Beta-lactoglobulin III)	0.25	-	cyt	0					162
O81852 UniProt NPD GO	AKH2_ARATH	Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplast precursor (AK-HD 2) (AK-HSDH 2) ( ...	0.25	-	mit	0	Plastid; chloroplast				916
P47853 UniProt NPD GO	PGS1_RAT	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1)	0.25	-	end	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				369
Q32WR5 UniProt NPD GO	BL1S2_RAT	Biogenesis of lysosome-related organelles complex-1 subunit 2 (Spinal cord-expressed protein 1)	0.25	-	nuc	0	Centrosome. Localizes to the centrosomes in a microtubule-dependent manner (By similarity)				142
P13019 UniProt NPD GO	BLMH_RABIT	Bleomycin hydrolase (EC 3.4.22.40) (BLM hydrolase) (BMH) (BH) (Fragment)	0.25	-	cyt	0	Cytoplasm				277
Q9GL27 UniProt NPD GO	BRAC_CANFA	Brachyury protein (T protein)	0.25	-	nuc	0	Nucleus				435
Q06225 UniProt NPD GO	BDNF_MACMU	Brain-derived neurotrophic factor (BDNF) (Fragment)	0.25	-	nuc	0	Secreted protein				114
P25430 UniProt NPD GO	BDNF_RAJCL	Brain-derived neurotrophic factor (BDNF) (Fragment)	0.25	-	nuc	0	Secreted protein				43
Q6LCI5 UniProt NPD GO	BDNF_AILME	Brain-derived neurotrophic factor precursor (BDNF)	0.25	-	nuc	0	Secreted protein				247
O18755 UniProt NPD GO	BDNF_PROLO	Brain-derived neurotrophic factor precursor (BDNF)	0.25	-	nuc	0	Secreted protein				247
Q6UXG8 UniProt NPD GO	BTNL9_HUMAN	Butyrophilin-like protein 9 precursor	0.25	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				535
P17992 UniProt NPD GO	HOR9_HORVU	C-hordein (Clone PC-919) (Fragment)	0.25	-	nuc	0					68
P02864 UniProt NPD GO	HORC_HORSP	C-hordein (Fragment)	0.25	-	nuc	0					28
Q8AYR5 UniProt NPD GO	ANFC2_ORYLA	C-type natriuretic peptide 2 precursor	0.25	-	nuc	0	Secreted protein				126
P56283 UniProt NPD GO	ANFC_SHEEP	C-type natriuretic peptide precursor [Contains: CNP-22; CNP-29; CNP-53]	0.25	-	exc	0	Secreted protein				126
Q28065 UniProt NPD GO	C4BP_BOVIN	C4b-binding protein alpha chain precursor (C4bp)	0.25	-	exc	0					610
Q91ZW7 UniProt NPD GO	C209E_MOUSE	CD209 antigen-like protein E (DC-SIGN-related protein 4) (DC-SIGNR4)	0.25	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				208
P81508 UniProt NPD GO	CHBBA_CROHO	CHH-B subunit alpha	0.25	-	cyt	0	Secreted protein				127
P16215 UniProt NPD GO	1C28_PANTR	CHLA class I histocompatibility antigen, CH28 alpha chain precursor	0.25	-	end	1	Membrane; single-pass type I membrane protein				346
Q9T045 UniProt NPD GO	CBL11_ARATH	COBRA-like protein 11 precursor	0.25	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				668
Q6CPB1 UniProt NPD GO	CSN12_KLULA	COP9 signalosome complex subunit 12	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				424
Q6P2U9 UniProt NPD GO	CSN3_BRARE	COP9 signalosome complex subunit 3 (Signalosome subunit 3)	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				423
P70698 UniProt NPD GO	PYRG1_MOUSE	CTP synthase 1 (EC 6.3.4.2) (UTP--ammonia ligase 1) (CTP synthetase 1)	0.25	-	cyt	0					591
Q9VGG5 UniProt NPD GO	CAD87_DROME	Cadherin 87A precursor	0.25	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			1975
Q12324 UniProt NPD GO	YVC1_YEAST	Calcium channel YVC1 (Yeast vacuolar conductance protein 1) (TRP homolog)	0.25	-	end	7	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole (sensu Fungi) [IDA]			675
P48593 UniProt NPD GO	E631_DROME	Calcium-binding protein E63-1	0.25	-	mit	0		cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			193
Q6ATV4 UniProt NPD GO	ACA2_ORYSA	Calcium-transporting ATPase 2, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 2)	0.25	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1033
Q9LF79 UniProt NPD GO	ACA8_ARATH	Calcium-transporting ATPase 8, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 8)	0.25	-	end	6	Cell membrane; multi-pass membrane protein				1074
P11798 UniProt NPD GO	KCC2A_MOUSE	Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.11.17) (CaM-kinase II alpha ...	0.25	-	nuc	0	Isoform Alpha KAP: Cytoplasm (Probable)	calcium- and calmodulin-dependent protein k... [TAS]		1HKX	478
P51911 UniProt NPD GO	CNN1_HUMAN	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.25	-	nuc	0			600806	1WYP	297
Q08093 UniProt NPD GO	CNN2_MOUSE	Calponin-2 (Calponin H2, smooth muscle) (Neutral calponin)	0.25	-	nuc	0					305
Q9JM47 UniProt NPD GO	CSEN_RAT	Calsenilin (DRE-antagonist modulator) (DREAM) (Kv channel-interacting protein 3) (A-type potassium c ...	0.25	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor. Endoplasmic reticulum. Golgi apparatus. In the presence of P ...				256
P41210 UniProt NPD GO	CATR_ATRNU	Caltractin (Centrin)	0.25	-	mit	0	Centrosome. Centrosome of interphase and mitotic cells				167
Q06827 UniProt NPD GO	CATR_SCHDU	Caltractin (Centrin)	0.25	-	mit	0					168
Q42435 UniProt NPD GO	CCS_CAPAN	Capsanthin/capsorubin synthase, chloroplast precursor (EC 5.3.99.8)	0.25	+	cyt	0	Plastid; chloroplast. Plastid; chromoplast				498
Q6QNM1 UniProt NPD GO	KC1_TOXGO	Casein kinase I (EC 2.7.11.1)	0.25	-	cyt	0					324
Q8N752 UniProt NPD GO	KC1AL_HUMAN	Casein kinase I isoform alpha-like (EC 2.7.11.1) (CKI-alpha-like) (CK1)	0.25	-	cyt	0	Cytoplasm (By similarity)				337
P28547 UniProt NPD GO	CSK2A_THEPA	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.25	-	cyt	0	Cytoplasm (By similarity)				348
O76485 UniProt NPD GO	CSK2B_SPOFR	Casein kinase II subunit beta (CK II beta)	0.25	-	cyt	0					221
P67868 UniProt NPD GO	CSK2B_BOVIN	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.25	-	cyt	0					215
P67869 UniProt NPD GO	CSK2B_CHICK	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.25	-	cyt	0					215
P67871 UniProt NPD GO	CSK2B_MOUSE	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.25	-	cyt	0					215
P67872 UniProt NPD GO	CSK2B_PIG	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.25	-	cyt	0					215
P67873 UniProt NPD GO	CSK2B_RABIT	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.25	-	cyt	0					215
P67874 UniProt NPD GO	CSK2B_RAT	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.25	-	cyt	0					215
P67870 UniProt NPD GO	CSK2B_HUMAN	Casein kinase II subunit beta (CK II beta) (Phosvitin) (G5a)	0.25	-	cyt	0		protein kinase CK2 complex [NAS]	115441	1QF8	215
Q9TV13 UniProt NPD GO	CASP1_HORSE	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.25	-	cyt	0	Cytoplasm				405
Q99MX7 UniProt NPD GO	CECR6_MOUSE	Cat eye syndrome critical region protein 6 homolog	0.25	+	nuc	3					572

You are viewing entries 45001 to 45050 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.