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
O22380 UniProt NPD GO	CADH_LOLPR	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.05	-	cyt	0					361
Q40976 UniProt NPD GO	CADH_PINRA	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.05	-	cyt	0					357
P41637 UniProt NPD GO	CADH_PINTA	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.05	-	cyt	0					357
P31657 UniProt NPD GO	CADH_POPDE	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.05	-	cyt	0					357
O82035 UniProt NPD GO	CADH2_PICAB	Cinnamyl alcohol dehydrogenase 2 (EC 1.1.1.195) (CAD 2)	0.05	-	cyt	0					357
Q08350 UniProt NPD GO	CADH7_PICAB	Cinnamyl alcohol dehydrogenase 7/8 (EC 1.1.1.195) (CAD 7/8)	0.05	-	cyt	0					357
P20115 UniProt NPD GO	CISY4_ARATH	Citrate synthase 4, mitochondrial precursor (EC 2.3.3.1)	0.05	-	mit	0	Mitochondrion; mitochondrial matrix				474
Q9M1D3 UniProt NPD GO	CISY5_ARATH	Citrate synthase 5, mitochondrial precursor (EC 2.3.3.1)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			433
O00098 UniProt NPD GO	CISY_EMENI	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.05	-	pox	0	Mitochondrion; mitochondrial matrix				474
Q99P82 UniProt NPD GO	CLD11_RAT	Claudin-11	0.05	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			207
Q60771 UniProt NPD GO	CLD11_MOUSE	Claudin-11 (Oligodendrocyte transmembrane protein) (Oligodendrocyte-specific protein)	0.05	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to plasma membrane [TAS] tight junction [ISS]			207
Q8BXA6 UniProt NPD GO	CLD17_MOUSE	Claudin-17	0.05	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			224
Q95KM6 UniProt NPD GO	CLD2_CANFA	Claudin-2	0.05	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			230
P57739 UniProt NPD GO	CLD2_HUMAN	Claudin-2 (SP82)	0.05	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]	300520		230
P00488 UniProt NPD GO	F13A_HUMAN	Coagulation factor XIII A chain precursor (EC 2.3.2.13) (Coagulation factor XIIIa) (Protein-glutamin ...	0.05	-	cyt	0	Cytoplasm. Secreted protein. Secreted into the blood plasma. Cytoplasmic in most tissues, but also s ...	extracellular region [TAS]	134570	1QRK	731
P02681 UniProt NPD GO	COAG_TACTR	Coagulogen precursor [Contains: Coagulin chain A; Peptide C; Coagulin chain B]	0.05	-	exc	0	Secreted protein			1AOC	195
P02746 UniProt NPD GO	C1QB_HUMAN	Complement C1q subcomponent subunit B precursor	0.05	-	vac	0	Secreted protein	complement component C1q complex [TAS]	120570	1PK6	251
Q02105 UniProt NPD GO	C1QC_MOUSE	Complement C1q subcomponent subunit C precursor	0.05	-	exc	0	Secreted protein				246
Q8K479 UniProt NPD GO	C1QT5_MOUSE	Complement C1q tumor necrosis factor-related protein 5 precursor	0.05	-	exc	0	Secreted protein (Probable)				243
Q5FVH0 UniProt NPD GO	C1QT5_RAT	Complement C1q tumor necrosis factor-related protein 5 precursor	0.05	-	exc	0	Secreted protein (Probable)				243
Q9ESN4 UniProt NPD GO	C1QL3_MOUSE	Complement C1q-like protein 3 precursor (Gliacolin)	0.05	-	exc	0	Secreted protein (Potential)				255
Q69DK8 UniProt NPD GO	C1S_PIG	Complement C1s subcomponent precursor (EC 3.4.21.42) (C1 esterase) [Contains: Complement C1s subcomp ...	0.05	-	exc	0					687
P81460 UniProt NPD GO	CONA_CANLI	Concanavalin A (Con A)	0.05	-	cyt	0					237
P14894 UniProt NPD GO	CONA_CANGL	Concanavalin A precursor (Con A)	0.05	-	exc	1 *					290
Q9R1E9 UniProt NPD GO	CTGF_RAT	Connective tissue growth factor precursor	0.05	-	exc	0	Secreted protein				347
P29268 UniProt NPD GO	CTGF_MOUSE	Connective tissue growth factor precursor (Protein FISP-12) (Hypertrophic chondrocyte-specific prote ...	0.05	-	exc	0	Secreted protein; extracellular space; extracellular matrix. Secreted protein	extracellular matrix (sensu Metazoa) [IDA] extracellular region [IDA]			348
P58623 UniProt NPD GO	CX1A_CONBE	Conotoxin BeTXIa	0.05	-		0	Secreted protein				14
P84698 UniProt NPD GO	CX13A_CONDE	Conotoxin de13a precursor (Fragment)	0.05	-	nuc	0	Secreted protein				34
Q39065 UniProt NPD GO	COPT1_ARATH	Copper transporter 1	0.05	-	mit	2	Membrane; multi-pass membrane protein (Potential)				170
O89046 UniProt NPD GO	COR1B_RAT	Coronin-1B (Coronin-2)	0.05	-	nuc	0	Localized to the leading edge in fibroblasts, as well as weakly along actin stress fibers (By simila ...				484
P00565 UniProt NPD GO	KCRM_CHICK	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.05	-	cyt	0	Cytoplasm				381
O57540 UniProt NPD GO	MYC1_CRODU	Crotamine CRO1 precursor	0.05	-	cyt	0	Secreted protein (By similarity)				65
Q9PWF3 UniProt NPD GO	MYC2_CRODU	Crotamine CRO2 precursor	0.05	-	cyt	0	Secreted protein (By similarity)				65
O73799 UniProt NPD GO	MYC3_CRODU	Crotamine CRO3 precursor	0.05	-	vac	0	Secreted protein (By similarity)				64
Q8QZT4 UniProt NPD GO	CRUM3_MOUSE	Crumbs protein homolog 3 precursor	0.05	-	end	2 *	Cell membrane; apical cell membrane; single-pass type I membrane protein (By similarity). Cell membr ...				113
P81032 UniProt NPD GO	CHH_CANPG	Crustacean hyperglycemic hormone (CHH)	0.05	-	cyt	0	Secreted protein				72
P81700 UniProt NPD GO	CHH6_PENJP	Crustacean hyperglycemic hormone 6 (Pej-SGP-VI)	0.05	-	cyt	0	Secreted protein				72
P15534 UniProt NPD GO	CRS3_NOTGO	Crystallin SIII (Fragment)	0.05	-	cyt	0					38
P29602 UniProt NPD GO	CPC_CUCSA	Cucumber peeling cupredoxin (CPC) (Stellacyanin)	0.05	-	nuc	0				1JER	137
P83355 UniProt NPD GO	CU14B_LIMPO	Cuticle protein 14 isoform b (LpCP14b)	0.05	-	cyt	0					130
P45586 UniProt NPD GO	CU79A_LOCMI	Cuticle protein 79, isoform A (LM-79A) (LM-ACP 79A)	0.05	-	nuc	1 *					131
P45587 UniProt NPD GO	CU79B_LOCMI	Cuticle protein 79, isoform B (LM-79B) (LM-ACP 79B)	0.05	-	nuc	1 *					131
P81575 UniProt NPD GO	CUPA1_CANPG	Cuticle protein AM/CP1114 (CPAM/CPAM1114)	0.05	-	cyt	0					102
P41744 UniProt NPD GO	CUTI_ALTBR	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.05	-	mit	0	Secreted protein				209
P10951 UniProt NPD GO	CUTI_COLCA	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.05	-	exc	0	Secreted protein				228
O22683 UniProt NPD GO	CYNS_ARATH	Cyanate hydratase (EC 4.2.1.104) (Cyanase) (Cyanate lyase) (Cyanate hydrolase)	0.05	-	cyt	0					168
O77617 UniProt NPD GO	CD2A1_MONDO	Cyclin-dependent kinase inhibitor 2A (Cyclin-dependent kinase 4 inhibitor A) (CDK4I) (p16-INK4) (p16 ...	0.05	-	nuc	0					171
Q9LM02 UniProt NPD GO	SMT1_ARATH	Cycloartenol-C-24-methyltransferase (EC 2.1.1.41) (24-sterol C-methyltransferase 1) (Sterol C-methyl ...	0.05	-	cyt	0					336
P32582 UniProt NPD GO	CBS_YEAST	Cystathionine beta-synthase (EC 4.2.1.22) (Serine sulfhydrase) (Beta-thionase)	0.05	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			507
Q28987 UniProt NPD GO	CYTA8_PIG	Cystatin A8 (Stefin A8)	0.05	-	cyt	0	Cytoplasm				103

You are viewing entries 74101 to 74150 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.