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
P58990 UniProt NPD GO	CXPH_CONRA	Conophysin-R	0.01	-	nuc	0	Secreted protein				84
P58805 UniProt NPD GO	RF1_CONSP	Conorfamide-Sr1	0.01	-		0	Secreted protein				12
P58624 UniProt NPD GO	CX1B_CONBE	Conotoxin BeTXIb	0.01	-		0	Secreted protein				15
P24160 UniProt NPD GO	CX7A_CONTE	Conotoxin TxVIIA (TxIIA)	0.01	-	nuc	0	Secreted protein				27
P69762 UniProt NPD GO	CX6E_CONVC	Conotoxin Vc6c precursor (Conotoxin Vc6.5)	0.01	-	exc	0	Secreted protein				77
P58849 UniProt NPD GO	CX5B_CONAL	Conotoxin au5b	0.01	-		0	Secreted protein				11
P0C1C9 UniProt NPD GO	CXO7A_CONDE	Conotoxin de7a	0.01	-	nuc	0	Secreted protein				28
P84705 UniProt NPD GO	CX14A_CONFF	Conotoxin flf14a	0.01	-	cyt	0	Secreted protein				27
P84706 UniProt NPD GO	CX14B_CONFF	Conotoxin flf14b	0.01	-	cyt	0	Secreted protein				27
P83437 UniProt NPD GO	COG5_BOVIN	Conserved oligomeric Golgi complex component 5 (GTC-90) (Fragments)	0.01	-	cyt	0	Cytoplasm; cytosol (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By ...				31
P13736 UniProt NPD GO	CIP1_MYTED	Contraction-inhibiting peptide 1 (MIP I)	0.01	-		0					6
P13737 UniProt NPD GO	CIP2_MYTED	Contraction-inhibiting peptide 2 (MIP II)	0.01	-		0					6
P58786 UniProt NPD GO	COW_CONRA	Contryphan precursor [Contains: Contryphan-R (Bromocontryphan); [Des-Gly1]-contryphan-R]	0.01	-	vac	0	Secreted protein			1QFB	63
Q9D8X1 UniProt NPD GO	CUTC_MOUSE	Copper homeostasis protein cutC homolog	0.01	-	cyt	0					272
O00244 UniProt NPD GO	ATOX1_HUMAN	Copper transport protein ATOX1 (Metal transport protein ATX1)	0.01	-	cyt	0			602270	1TL5	68
Q5BIN6 UniProt NPD GO	CNIH_BOVIN	Cornichon homolog	0.01	-	end	3 *	Membrane; multi-pass membrane protein (By similarity)				144
Q5RDB5 UniProt NPD GO	CNIH_PONPY	Cornichon homolog	0.01	-	end	3 *	Membrane; multi-pass membrane protein (By similarity)				144
O95406 UniProt NPD GO	CNIH_HUMAN	Cornichon homolog (TGAM77)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				144
P41237 UniProt NPD GO	CTXN1_RAT	Cortexin-1	0.01	-	nuc	1 *					82
Q6QLL4 UniProt NPD GO	DHI1_CAVPO	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.01	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein			1XSE	299
P28845 UniProt NPD GO	DHI1_HUMAN	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.01	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum membrane [IDA]	600713	2BEL	291
Q7M3I4 UniProt NPD GO	DHI1_RABIT	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.01	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Microso ...	endoplasmic reticulum membrane [NAS] microsome [IDA]			291
Q29608 UniProt NPD GO	DHI1_SAISC	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.01	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				290
P82601 UniProt NPD GO	TXVL2_CORVA	Covalitoxin-2 (Covalitoxin-II) (CvTx-II)	0.01	-	nuc	0	Secreted protein				31
P01518 UniProt NPD GO	CRBL_VESCR	Crabrolin	0.01	-		0	Secreted protein				13
P01542 UniProt NPD GO	CRAM_CRAAB	Crambin	0.01	-	nuc	0	Secreted protein			2EYD	46
P26460 UniProt NPD GO	KCRB_SQUAC	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK) (Fragments)	0.01	-	cyt	0	Cell membrane; basal cell membrane. Basal membrane of the sodium chloride-secreting epithelia				52
P08878 UniProt NPD GO	PA2A_CRODU	Crotoxin acid chain precursor (CA) (Crotapotin) [Contains: Crotoxin chain A; Crotoxin chain B; Croto ...	0.01	-	exc	0	Secreted protein				138
P83485 UniProt NPD GO	CHHA_CHEDE	Crustacean hyperglycemic hormone A (CHHA)	0.01	-	cyt	0	Secreted protein	extracellular region [NAS]			72
P58989 UniProt NPD GO	CRA1_HOMGA	Crustacyanin-A1 subunit	0.01	-	nuc	0	Secreted protein; extracellular space			1S44	181
P80029 UniProt NPD GO	CRC1_HOMGA	Crustacyanin-C1 subunit	0.01	-	cyt	0	Secreted protein; extracellular space			1S2P	181
P83619 UniProt NPD GO	TXC1A_CUPSA	Cupiennin-1a	0.01	-	cyt	0	Secreted protein				35
P83620 UniProt NPD GO	TXC1B_CUPSA	Cupiennin-1b	0.01	-	cyt	0	Secreted protein				35
P83621 UniProt NPD GO	TXC1C_CUPSA	Cupiennin-1c	0.01	-	cyt	0	Secreted protein				35
P11735 UniProt NPD GO	CU30_LOCMI	Cuticle protein 30 (LM-30) (LM-ACP 30) (Fragment)	0.01	-		0					10
P80232 UniProt NPD GO	CU70_LOCMI	Cuticle protein 70, isoforms A and B (LM-70A/LM-70B)	0.01	-	mit	2 *					88
P82122 UniProt NPD GO	CUO9_BLACR	Cuticle protein 9 (BcNCP3.8)	0.01	-	cyt	0					34
P81580 UniProt NPD GO	CUPC1_CANPG	Cuticle protein CP1158 (CPCP1158)	0.01	-	cyt	0					114
P81582 UniProt NPD GO	CUPC3_CANPG	Cuticle protein CP1246 (CPCP1246)	0.01	-	cyt	0					117
P11373 UniProt NPD GO	CUTI_COLGL	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.01	-	exc	0	Secreted protein				224
Q8TGB8 UniProt NPD GO	CUTI_MONFR	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.01	-	vac	0	Secreted protein (By similarity)				201
Q9Y7G8 UniProt NPD GO	CUTI_PYRBR	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.01	-	cyt	0	Secreted protein (By similarity)				203
Q60772 UniProt NPD GO	CDN2C_MOUSE	Cyclin-dependent kinase 6 inhibitor (p18-INK6) (Cyclin-dependent kinase 4 inhibitor C) (p18-INK4c)	0.01	-	cyt	0					168
P84647 UniProt NPD GO	HYFLA_HYBFL	Cyclotide Hyfl A	0.01	-	cyt	0					31
P84649 UniProt NPD GO	HYFLC_HYBFL	Cyclotide Hyfl C	0.01	-	nuc	0					32
P58445 UniProt NPD GO	HYPAA_HYBPA	Cyclotide hypa A	0.01	-	nuc	0					30
P84635 UniProt NPD GO	CYVA_VIOCT	Cyclotide vico A	0.01	-	nuc	0					31
P84636 UniProt NPD GO	CYVB_VIOCT	Cyclotide vico B	0.01	-	nuc	0					31
P58433 UniProt NPD GO	CYH1_VIOHE	Cycloviolacin-H1	0.01	-	nuc	0					30
P58437 UniProt NPD GO	CYO5_VIOOD	Cycloviolacin-O5	0.01	-	nuc	0					30

You are viewing entries 87201 to 87250 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.