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
P60015 UniProt NPD GO	OPSB_PANTR	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment)	0.04	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				348
Q9Y3E2 UniProt NPD GO	BOLA1_HUMAN	BolA-like protein 1	0.04	-	exc	0					137
Q5RCE5 UniProt NPD GO	BOLA1_PONPY	BolA-like protein 1	0.04	-	exc	0					137
P26729 UniProt NPD GO	BXA6_BOMMO	Bombyxin A-6 precursor (BBX-A6) (Bombyxin-II) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: B ...	0.04	-	vac	0	Secreted protein			1BON	92
Q17194 UniProt NPD GO	BXB10_BOMMO	Bombyxin B-10 precursor (BBX-B10) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-10 ...	0.04	-	cyt	0	Secreted protein				87
P26736 UniProt NPD GO	BXD1_BOMMO	Bombyxin D-1 precursor (BBX-D1) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin D-1 B ...	0.04	-	cyt	0	Secreted protein				90
O61271 UniProt NPD GO	BXG1_BOMMO	Bombyxin G-1 precursor (BBX-G1) [Contains: Bombyxin G-1 B chain; Bombyxin G-1 A chain]	0.04	-	vac	0	Secreted protein				90
Q9D023 UniProt NPD GO	BR44_MOUSE	Brain protein 44	0.04	-	cyt	0		mitochondrion [IDA]			127
P38718 UniProt NPD GO	BR44_RAT	Brain protein 44 (0-44 protein)	0.04	-	cyt	0					127
Q9GZN4 UniProt NPD GO	BSSP4_HUMAN	Brain-specific serine protease 4 precursor (EC 3.4.21.-) (BSSP-4) (Serine protease 22) (Tryptase eps ...	0.04	-	vac	0	Secreted protein		609343		317
P47176 UniProt NPD GO	BCA2_YEAST	Branched-chain-amino-acid aminotransferase, cytosolic (EC 2.6.1.42) (BCAT) (TWT2 protein)	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			376
P82233 UniProt NPD GO	BR1TA_RANTE	Brevinin-1Ta	0.04	-		0	Secreted protein				17
P80554 UniProt NPD GO	BULB_NARPS	Bulb protein (Fragment)	0.04	-		0					20
P18892 UniProt NPD GO	BT1A1_BOVIN	Butyrophilin subfamily 1 member A1 precursor (BT)	0.04	-	end	1	Membrane; single-pass type I membrane protein				526
Q08280 UniProt NPD GO	BSC6_YEAST	Bypass of stop codon protein 6	0.04	-	end	11	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; multi-pass membrane protein (Probabl ...				497
P53045 UniProt NPD GO	ERG25_YEAST	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase)	0.04	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Probable)	endoplasmic reticulum membrane [IDA] plasma membrane [IDA]			309
Q8J207 UniProt NPD GO	ERG3_LEPMC	C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase)	0.04	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				356
Q9WUT7 UniProt NPD GO	CCR9_MOUSE	C-C chemokine receptor type 9 (C-C CKR-9) (CC-CKR-9) (CCR-9) (Chemokine C-C receptor 10)	0.04	-	end	7	Membrane; multi-pass membrane protein				369
Q5MD61 UniProt NPD GO	CXCR3_BOVIN	C-X-C chemokine receptor type 3 (CXC-R3) (CXCR-3) (Interferon-inducible protein 10 receptor) (IP-10 ...	0.04	-	end	7	Membrane; multi-pass membrane protein (By similarity)				366
Q9TV16 UniProt NPD GO	CXCR6_PANTR	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo) (G-protein coup ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein				342
O00574 UniProt NPD GO	CXCR6_HUMAN	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo) (G-protein coup ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	605163		342
P05730 UniProt NPD GO	PHCA_CYAPA	C-phycocyanin alpha chain	0.04	-	cyt	0	Plastid; cyanelle				162
P14847 UniProt NPD GO	CRP_MOUSE	C-reactive protein precursor	0.04	-	vac	0	Secreted protein				225
O19062 UniProt NPD GO	CRP_PIG	C-reactive protein precursor	0.04	-	exc	0	Secreted protein (By similarity)				222
Q13363 UniProt NPD GO	CTBP1_HUMAN	C-terminal-binding protein 1 (EC 1.1.1.-) (CtBP1)	0.04	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)		602618	1MX3	440
Q4PRC7 UniProt NPD GO	CLEC6_DABRU	C-type lectin-like protein subunit 6 precursor	0.04	-	end	0	Secreted protein (Potential)				144
P30992 UniProt NPD GO	C5AR_CANFA	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				352
P61170 UniProt NPD GO	CD151_CERAE	CD151 antigen (Platelet-endothelial tetraspan antigen 3) (PETA-3)	0.04	-	end	4 *	Membrane; multi-pass membrane protein				253
P61171 UniProt NPD GO	CD151_MACMU	CD151 antigen (Platelet-endothelial tetraspan antigen 3) (PETA-3)	0.04	-	end	4 *	Membrane; multi-pass membrane protein				253
P48509 UniProt NPD GO	CD151_HUMAN	CD151 antigen (Platelet-endothelial tetraspan antigen 3) (PETA-3) (GP27) (Membrane glycoprotein SFA- ...	0.04	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS] plasma membrane [NAS]	609057		253
P51447 UniProt NPD GO	CD59_AOTTR	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.04	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				128
P40239 UniProt NPD GO	CD9_FELCA	CD9 antigen	0.04	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			225
P40241 UniProt NPD GO	CD9_RAT	CD9 antigen	0.04	-	end	4 *	Membrane; multi-pass membrane protein	cell surface [IDA] integral to plasma membrane [ISS]			225
P08456 UniProt NPD GO	PSS_YEAST	CDP-diacylglycerol--serine O-phosphatidyltransferase (EC 2.7.8.8) (Phosphatidylserine synthase)	0.04	-	end	2	Microsome. Mitochondrion; mitochondrial outer membrane; peripheral membrane protein				275
P97325 UniProt NPD GO	SIAT6_MOUSE	CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.6) (N-acetyllact ...	0.04	-	vac	1 *	Membrane; single-pass type II membrane protein				374
Q02734 UniProt NPD GO	SIAT6_RAT	CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.6) (N-acetyllact ...	0.04	-	vac	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				374
P36104 UniProt NPD GO	SWD2_YEAST	COMPASS component SWD2 (Complex proteins associated with SET1 protein SWD2) (Set1C component SWD2)	0.04	-	mit	0	Nucleus	COMPASS complex [IPI] mRNA cleavage and polyadenylation specifici... [IPI]			329
P68354 UniProt NPD GO	CSN5A_BRAOL	COP9 signalosome complex subunit 5a (EC 3.4.-.-) (Signalosome subunit 5a) (Jun activation domain-bin ...	0.04	-	nuc	0	Cytoplasm. Nucleus				34
O42644 UniProt NPD GO	PYRG_SCHPO	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.04	-	cyt	0					600
O55075 UniProt NPD GO	CADH2_CRIGR	Cadherin-2 (Neural-cadherin) (N-cadherin) (CDw325 antigen) (Fragment)	0.04	-	cyt	0	Membrane; single-pass type I membrane protein (By similarity)				238
P01265 UniProt NPD GO	CALC3_ONCKI	Calcitonin-3	0.04	-	nuc	0	Secreted protein				32
Q9M7R0 UniProt NPD GO	ALL8_OLEEU	Calcium-binding allergen Ole e 8 (PCA18/PCA23)	0.04	-	nuc	0					171
P13566 UniProt NPD GO	CABP_SCHMA	Calcium-binding protein (CaBP)	0.04	-	nuc	0					69
P15156 UniProt NPD GO	CASP_MESAU	Calcium-dependent serine proteinase precursor (EC 3.4.21.-) (CASP) [Contains: Calcium-dependent seri ...	0.04	-	vac	0					695
P41868 UniProt NPD GO	FARD_CALVO	CalliFMRFamide-13	0.04	-		0	Secreted protein				9
P41857 UniProt NPD GO	FAR2_CALVO	CalliFMRFamide-2	0.04	-		0	Secreted protein				9
P41858 UniProt NPD GO	FAR3_CALVO	CalliFMRFamide-3	0.04	-		0	Secreted protein				9
P41861 UniProt NPD GO	FAR6_CALVO	CalliFMRFamide-6	0.04	-		0	Secreted protein				9
P93087 UniProt NPD GO	CALM_CAPAN	Calmodulin (CaM)	0.04	-	cyt	0					148
Q7Y052 UniProt NPD GO	CALM_EUPCH	Calmodulin (CaM)	0.04	-	cyt	0					148

You are viewing entries 76401 to 76450 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.