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
O08520 UniProt NPD GO	S35A1_CRIGR	CMP-sialic acid transporter (CMP-Sia-Tr) (CMP-SA-Tr) (Solute carrier family 35 member A1)	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				336
P78382 UniProt NPD GO	S35A1_HUMAN	CMP-sialic acid transporter (CMP-Sia-Tr) (CMP-SA-Tr) (Solute carrier family 35 member A1)	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [TAS] integral to plasma membrane [TAS]	605634		337
Q61420 UniProt NPD GO	S35A1_MOUSE	CMP-sialic acid transporter (CMP-Sia-Tr) (CMP-SA-Tr) (Solute carrier family 35 member A1)	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				336
Q6NUC2 UniProt NPD GO	CSN6_XENLA	COP9 signalosome complex subunit 6 (Signalosome subunit 6)	0.00	-	mit	1 *	Cytoplasm (By similarity). Nucleus (By similarity)				318
O88545 UniProt NPD GO	CSN6_MOUSE	COP9 signalosome complex subunit 6 (Signalosome subunit 6) (SGN6) (JAB1-containing signalosome subun ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	signalosome complex [IDA]			324
Q7L5N1 UniProt NPD GO	CSN6_HUMAN	COP9 signalosome complex subunit 6 (Signalosome subunit 6) (SGN6) (JAB1-containing signalosome subun ...	0.00	-	cyt	0	Nucleus. Cytoplasm. The interaction with HIV-1 Vpr protein possibly leads its translocation to a per ...				327
Q9H4G8 UniProt NPD GO	ZCSL1_HUMAN	CSL-type zinc finger-containing protein 1	0.00	-	cyt	0					78
P42735 UniProt NPD GO	CDI8_ARATH	Cadmium-induced protein AS8	0.00	-	cyt	2 *					171
P62567 UniProt NPD GO	CD11_LITCH	Caeridin-1.1/1.2/1.3	0.00	-		0	Secreted protein				12
P62566 UniProt NPD GO	CD11_LITGI	Caeridin-1.1/1.2/1.3	0.00	-		0	Secreted protein				12
P62565 UniProt NPD GO	CDN11_LITSP	Caeridin-1.1/1.2/1.3	0.00	-		0	Secreted protein				12
P62564 UniProt NPD GO	CDN11_LITXA	Caeridin-1.1/1.2/1.3	0.00	-		0	Secreted protein				12
P62581 UniProt NPD GO	CDN14_LITCH	Caeridin-1.4	0.00	-		0	Secreted protein				12
P62582 UniProt NPD GO	CDN14_LITXA	Caeridin-1.4	0.00	-		0	Secreted protein				12
P56247 UniProt NPD GO	CDN2_LITGI	Caeridin-2	0.00	-		0	Secreted protein				15
P56248 UniProt NPD GO	CDN3_LITGI	Caeridin-3	0.00	-		0	Secreted protein				15
P82076 UniProt NPD GO	CDN4_LITCE	Caeridin-4	0.00	-		0	Secreted protein				15
P82078 UniProt NPD GO	CDN6_LITCE	Caeridin-6	0.00	-		0	Secreted protein				15
P82051 UniProt NPD GO	CDN71_LITEW	Caeridin-7.1	0.00	-		0	Secreted protein				13
P62568 UniProt NPD GO	CR11_LITSP	Caerin-1.1 [Contains: Caerin-1.1.1; Caerin-1.1.2]	0.00	-	cyt	0	Secreted protein				25
P62569 UniProt NPD GO	CR11_LITGI	Caerin-1.1 [Contains: Caerin-1.1.1; Caerin-1.1.3; Caerin-1.1.5; Caerin-1.1.6; Caerin-1.1.7; Caerin-1 ...	0.00	-	cyt	0	Secreted protein				25
P82104 UniProt NPD GO	CR110_LITSP	Caerin-1.10	0.00	-	cyt	0	Secreted protein				25
P56227 UniProt NPD GO	CR12_LITCE	Caerin-1.2	0.00	-	cyt	0	Secreted protein				25
P56228 UniProt NPD GO	CR13_LITCE	Caerin-1.3	0.00	-	cyt	0	Secreted protein				25
P62545 UniProt NPD GO	CR14_LITCE	Caerin-1.4 [Contains: Caerin-1.4.1]	0.00	-	cyt	0	Secreted protein				25
P62544 UniProt NPD GO	CR14_LITGI	Caerin-1.4 [Contains: Caerin-1.4.1]	0.00	-	cyt	0	Secreted protein				25
P56230 UniProt NPD GO	CR15_LITCE	Caerin-1.5	0.00	-	cyt	0	Secreted protein				25
P62547 UniProt NPD GO	CR16_LITCH	Caerin-1.6 [Contains: Caerin-1.6.1]	0.00	-	cyt	0	Secreted protein				24
P62546 UniProt NPD GO	CR16_LITXA	Caerin-1.6 [Contains: Caerin-1.6.1]	0.00	-	cyt	0	Secreted protein				24
P62549 UniProt NPD GO	CR17_LITCH	Caerin-1.7 [Contains: Caerin-1.7.1]	0.00	-	cyt	0	Secreted protein				24
P62548 UniProt NPD GO	CR17_LITXA	Caerin-1.7 [Contains: Caerin-1.7.1]	0.00	-	cyt	0	Secreted protein				24
P81251 UniProt NPD GO	CR18_LITCH	Caerin-1.8	0.00	-	cyt	0	Secreted protein				24
P81252 UniProt NPD GO	CR19_LITCH	Caerin-1.9	0.00	-	cyt	0	Secreted protein				24
P56233 UniProt NPD GO	CR21_LITSP	Caerin-2.1	0.00	-	cyt	0	Secreted protein				25
P62571 UniProt NPD GO	CR22_LITCE	Caerin-2.2 [Contains: Caerin-2.2.1]	0.00	-	cyt	0	Secreted protein				25
P62570 UniProt NPD GO	CR22_LITGI	Caerin-2.2 [Contains: Caerin-2.2.1]	0.00	-	cyt	0	Secreted protein				25
P69032 UniProt NPD GO	CR23_LITCE	Caerin-2.3	0.00	-	cyt	0	Secreted protein				25
P56236 UniProt NPD GO	CR24_LITCE	Caerin-2.4	0.00	-	cyt	0	Secreted protein				25
P56237 UniProt NPD GO	CR25_LITGI	Caerin-2.5	0.00	-	cyt	0	Secreted protein				25
P62563 UniProt NPD GO	CR31_LITGI	Caerin-3.1	0.00	-	cyt	0	Secreted protein				22
P62562 UniProt NPD GO	CR31_LITSP	Caerin-3.1	0.00	-	cyt	0	Secreted protein				22
P56239 UniProt NPD GO	CR32_LITCE	Caerin-3.2	0.00	-	cyt	0	Secreted protein				22
P56240 UniProt NPD GO	CR33_LITCE	Caerin-3.3	0.00	-	cyt	0	Secreted protein				22
P56241 UniProt NPD GO	CR34_LITCE	Caerin-3.4	0.00	-	cyt	0	Secreted protein				22
P56264 UniProt NPD GO	CAER_LITXA	Caerulein	0.00	-		0	Secreted protein				10
P62541 UniProt NPD GO	CAE12_LITSP	Caerulein-1.2	0.00	-		0	Secreted protein				10
P62540 UniProt NPD GO	CAE12_LITCI	Caerulein-1.2/1.2Y4	0.00	-		0	Secreted protein				10
P82089 UniProt NPD GO	CAE31_LITCI	Caerulein-3.1/3.1Y4	0.00	-		0	Secreted protein				11
P82090 UniProt NPD GO	CAE32_LITCI	Caerulein-3.2/3.2Y4	0.00	-		0	Secreted protein				11
Q9FQY8 UniProt NPD GO	COMT1_CAPAN	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	nuc	0					359

You are viewing entries 92951 to 93000 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.