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
P16279 UniProt NPD GO	BGAM_HUMAN	Beta-galactosidase-related protein precursor (Beta-galactosidase-like protein) (S-Gal) (Elastin-bind ...	0.11	-	exc	0	Cytoplasm; perinuclear region. Localized to the perinuclear area of the cytoplasm but not to lysosom ...		230500		546
P07337 UniProt NPD GO	BGLS_KLUMA	Beta-glucosidase precursor (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrolase ...	0.11	-	cyt	0					845
Q15488 UniProt NPD GO	GUSL4_HUMAN	Beta-glucuronidase-like protein SMA5	0.11	-	cyt	0					140
O08540 UniProt NPD GO	MSMB_MOUSE	Beta-microseminoprotein precursor (Prostate secreted seminal plasma protein) (Prostate secretory pro ...	0.11	-	nuc	0	Secreted protein. Sperm surface (By similarity)				113
P56817 UniProt NPD GO	BACE1_HUMAN	Beta-secretase 1 precursor (EC 3.4.23.46) (Beta-site APP cleaving enzyme 1) (Beta-site amyloid precu ...	0.11	-	cyt	1	Membrane; single-pass type I membrane protein	endosome [IDA] Golgi apparatus [IDA] integral to plasma membrane [TAS]	604252	2G94	501
P45350 UniProt NPD GO	DRTS_DAUCA	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.11	-	cyt	0					528
P54113 UniProt NPD GO	PUR91_YEAST	Bifunctional purine biosynthesis protein ADE16 [Includes: Phosphoribosylaminoimidazolecarboxamide fo ...	0.11	-	cyt	0		cytosol [IDA]			591
P31939 UniProt NPD GO	PUR9_HUMAN	Bifunctional purine biosynthesis protein PURH [Includes: Phosphoribosylaminoimidazolecarboxamide for ...	0.11	-	cyt	0			601731	1PL0	592
Q9CWJ9 UniProt NPD GO	PUR9_MOUSE	Bifunctional purine biosynthesis protein PURH [Includes: Phosphoribosylaminoimidazolecarboxamide for ...	0.11	-	mit	0					592
O74928 UniProt NPD GO	PUR9_SCHPO	Bifunctional purine biosynthesis protein ade10 [Includes: Phosphoribosylaminoimidazolecarboxamide fo ...	0.11	-	cyt	0					585
P48445 UniProt NPD GO	BPL1_YEAST	Biotin--protein ligase (EC 6.3.4.-) (Biotin Apo-protein ligase) [Includes: Biotin--[methylmalonyl-Co ...	0.11	-	cyt	0		cytoplasm [IDA] intracellular [NAS]			690
O89106 UniProt NPD GO	FHIT_MOUSE	Bis(5'-adenosyl)-triphosphatase (EC 3.6.1.29) (Diadenosine 5',5'''-P1,P3-triphosphate hydrolase) (Di ...	0.11	-	cyt	0	Cytoplasm	cytoplasm [IDA]			149
P01065 UniProt NPD GO	IBB_VICAN	Bowman-Birk type proteinase inhibitor (VAI)	0.11	-	nuc	0					72
P02684 UniProt NPD GO	BNC2_RAT	Brain neuron cytoplasmic protein 2	0.11	-	mit	0	Cytoplasm				119
O15382 UniProt NPD GO	BCAT2_HUMAN	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT(m)) (Placent ...	0.11	-	mit	0	Isoform A: Mitochondrion. Isoform B: Cytoplasm	mitochondrion [TAS]	113530	1KTA	392
P32412 UniProt NPD GO	BR1E_RANES	Brevinin-1E precursor	0.11	-	exc	0	Secreted protein				71
Q8WVV5 UniProt NPD GO	BT2A2_HUMAN	Butyrophilin subfamily 2 member A2 precursor	0.11	-	end	3 *	Membrane; multi-pass membrane protein (By similarity)				523
Q5R996 UniProt NPD GO	BT3A3_PONPY	Butyrophilin subfamily 3 member A3 precursor	0.11	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				585
P51683 UniProt NPD GO	CCR2_MOUSE	C-C chemokine receptor type 2 (C-C CKR-2) (CC-CKR-2) (CCR-2) (CCR2) (JE/FIC receptor) (MCP-1 recepto ...	0.11	-	end	6	Membrane; multi-pass membrane protein				373
Q64H34 UniProt NPD GO	CCR3_CANFA	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				359
Q5ECR9 UniProt NPD GO	CCR5_CANFA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.11	-	end	6 *	Membrane; multi-pass membrane protein				352
O08556 UniProt NPD GO	CCR5_RAT	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (MIP-1 alpha receptor) (CD195 antigen)	0.11	-	end	6 *	Membrane; multi-pass membrane protein	endosome [IDA]			354
P51685 UniProt NPD GO	CCR8_HUMAN	C-C chemokine receptor type 8 (C-C CKR-8) (CC-CKR-8) (CCR-8) (GPR-CY6) (GPRCY6) (Chemokine receptor- ...	0.11	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601834		355
P00306 UniProt NPD GO	PHCA_GALSU	C-phycocyanin alpha chain	0.11	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome rod			1PHN	162
P00311 UniProt NPD GO	PHCB_GALSU	C-phycocyanin beta chain	0.11	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome rod			1PHN	172
O46036 UniProt NPD GO	CTBP_DROME	C-terminal-binding protein (CtBP protein) (dCtBP)	0.11	-	nuc	0	Nucleus				476
Q9ULY5 UniProt NPD GO	CLC4E_HUMAN	C-type lectin domain family 4 member E (C-type lectin superfamily member 9) (Macrophage-inducible C- ...	0.11	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)		609962		219
Q9UJ71 UniProt NPD GO	CLC4K_HUMAN	C-type lectin domain family 4 member K (Langerin) (CD207 antigen)	0.11	-	mit	1 *	Membrane; single-pass type II membrane protein. Found in Birbeck granules (BGs), which are organelle ...	endocytic vesicle [TAS]	604862		328
P84715 UniProt NPD GO	ANF39_ORNAN	C-type natriuretic peptide 39 (ovCNP-39)	0.11	-	nuc	0	Secreted protein	extracellular region [IDA]			39
Q68EV1 UniProt NPD GO	CD276_XENLA	CD276 antigen homolog precursor	0.11	-	end	1	Membrane; single-pass type I membrane protein (Probable)				308
Q9I8D8 UniProt NPD GO	CD40L_CHICK	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.11	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			272
O77541 UniProt NPD GO	CD59_RABIT	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				124
Q6X4A2 UniProt NPD GO	CIPK1_ORYSA	CIPK-like protein 1 (EC 2.7.11.1) (OsCK1)	0.11	-	nuc	0					449
Q4WJX0 UniProt NPD GO	CSN12_ASPFU	COP9 signalosome complex subunit 12	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				455
P91001 UniProt NPD GO	CSN5_CAEEL	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5) (JAB1 homolog)	0.11	-	nuc	0	Cytoplasm. Nucleus				368
P58465 UniProt NPD GO	CTDSL_MOUSE	CTD small phosphatase-like protein (CTDSP-like) (Small C-terminal domain phosphatase 3) (Nuclear LIM ...	0.11	-	cyt	0	Nucleus (Potential)				276
Q1RMS2 UniProt NPD GO	PYRG2_BOVIN	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2)	0.11	-	cyt	0					586
P70303 UniProt NPD GO	PYRG2_MOUSE	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2) (CTPsH)	0.11	-	cyt	0					586
P55288 UniProt NPD GO	CAD11_MOUSE	Cadherin-11 precursor (Osteoblast-cadherin) (OB-cadherin) (OSF-4)	0.11	-	nuc	1	Membrane; single-pass type I membrane protein	cytoplasm [IDA] plasma membrane [IDA]		2A4E	796
P33150 UniProt NPD GO	CAD13_CHICK	Cadherin-13 precursor (Truncated-cadherin) (T-cadherin) (T-cad)	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				712
Q6BWS8 UniProt NPD GO	CANB_DEBHA	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.11	-	cyt	0					174
P79222 UniProt NPD GO	CALCR_RABIT	Calcitonin receptor precursor (CT-R)	0.11	-	end	7	Membrane; multi-pass membrane protein				474
P97678 UniProt NPD GO	KCMB1_RAT	Calcium-activated potassium channel subunit beta 1 (Calcium-activated potassium channel, subfamily M ...	0.11	-	end	2 *	Membrane; multi-pass membrane protein				190
Q710D7 UniProt NPD GO	CABYR_VULVU	Calcium-binding tyrosine phosphorylation-regulated protein (Sperm protein 13) (fSP13 autoantigen)	0.11	-	cyt	0	Cytoplasm. Localized to fibrous sheath of the principal piece of sperm flagella				498
Q9SY55 UniProt NPD GO	ECA3_ARATH	Calcium-transporting ATPase 3, endoplasmic reticulum-type (EC 3.6.3.8)	0.11	-	end	8	Membrane; multi-pass membrane protein				998
Q9P7I2 UniProt NPD GO	KCC1_SCHPO	Calcium/calmodulin-dependent protein kinase type I (EC 2.7.11.17) (CaMK-I)	0.11	-	cyt	0	Cytoplasm				335
Q6Q487 UniProt NPD GO	CALX_ASPFU	Calnexin homolog precursor	0.11	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				563
P27825 UniProt NPD GO	CALX_YEAST	Calnexin homolog precursor	0.11	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	integral to endoplasmic reticulum membrane [IDA]			502
O88456 UniProt NPD GO	CPNS1_MOUSE	Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent prote ...	0.11	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon c ...				269
Q9SP22 UniProt NPD GO	CALR_MAIZE	Calreticulin precursor	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				420

You are viewing entries 62401 to 62450 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.