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
P46513 UniProt NPD GO	CAH2_FLALI	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonate dehydratase 2) (Fragment)	0.01	-	cyt	0	Cytoplasm (Potential)				190
P27140 UniProt NPD GO	CAHC_ARATH	Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase)	0.01	-	mit	0	Plastid; chloroplast; chloroplast stroma				347
P16016 UniProt NPD GO	CAHC_SPIOL	Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase)	0.01	-	mit	0	Plastid; chloroplast; chloroplast stroma				319
P00729 UniProt NPD GO	CBPY_YEAST	Carboxypeptidase Y precursor (EC 3.4.16.5) (Carboxypeptidase YSCY)	0.01	-	vac	0	Vacuole. Lysosome-like vacuoles	cytoplasm [IDA] endoplasmic reticulum [IDA] vacuolar lumen (sensu Fungi) [TAS]		1YSC	532
Q5EPH2 UniProt NPD GO	TCI1_RHIBU	Carboxypeptidase inhibitor precursor (TCI)	0.01	-	exc	0	Secreted protein				97
P81817 UniProt NPD GO	ALL14_CARMA	Carcinustatin-14	0.01	-		0	Secreted protein				5
P81818 UniProt NPD GO	ALL15_CARMA	Carcinustatin-15	0.01	-		0	Secreted protein				8
P81819 UniProt NPD GO	ALL16_CARMA	Carcinustatin-16	0.01	-		0	Secreted protein				8
P81805 UniProt NPD GO	ALL2_CARMA	Carcinustatin-2	0.01	-		0	Secreted protein				7
P81806 UniProt NPD GO	ALL3_CARMA	Carcinustatin-3	0.01	-		0	Secreted protein				7
P81808 UniProt NPD GO	ALL5_CARMA	Carcinustatin-5	0.01	-		0	Secreted protein				7
P81809 UniProt NPD GO	ALL7_CARMA	Carcinustatin-7 [Contains: Carcinustatin-6; Carcinustatin-1]	0.01	-		0	Secreted protein				8
P81811 UniProt NPD GO	ALL8_CARMA	Carcinustatin-8	0.01	-		0	Secreted protein				8
P81812 UniProt NPD GO	ALL9_CARMA	Carcinustatin-9	0.01	-		0	Secreted protein				8
P84119 UniProt NPD GO	CCAP_CARMA	Cardioactive peptide (CCAP) (Crustacean cardioactive peptide)	0.01	-		0	Secreted protein	extracellular region [ISS]			9
P84121 UniProt NPD GO	CCAP_SPOER	Cardioactive peptide (CCAP) (Crustacean cardioactive peptide)	0.01	-		0	Secreted protein (By similarity)	extracellular region [ISS]			9
P84120 UniProt NPD GO	CCAP_TENMO	Cardioactive peptide (CCAP) (Crustacean cardioactive peptide)	0.01	-		0	Secreted protein (By similarity)	extracellular region [ISS]			9
P58648 UniProt NPD GO	OCP1_OCTMI	Cardioactive peptides Ocp-1/Ocp-2	0.01	-		0	Secreted protein				4
Q9W6W6 UniProt NPD GO	CTX10_NAJAT	Cardiotoxin 10 precursor	0.01	-	mit	1 *	Secreted protein				82
P79810 UniProt NPD GO	CX1C_NAJAT	Cardiotoxin 1c precursor	0.01	-	mit	0	Secreted protein				81
Q9PST3 UniProt NPD GO	CTX2B_NAJSP	Cardiotoxin 2b precursor (CTX-2b) (Ctx2b)	0.01	-	mit	0	Secreted protein				81
Q9W6W9 UniProt NPD GO	CTX4N_NAJAT	Cardiotoxin 4N precursor (CTX-4N)	0.01	-	mit	0	Secreted protein				81
O73858 UniProt NPD GO	CTX6_NAJSP	Cardiotoxin 6 precursor (CTX-6) (Ctx6) (Fragment)	0.01	-	nuc	0	Secreted protein (By similarity)				62
O73859 UniProt NPD GO	CTX7_NAJSP	Cardiotoxin 7 precursor (CTX-7) (Ctx7) (Fragment)	0.01	-	nuc	0	Secreted protein (By similarity)				62
Q91135 UniProt NPD GO	CX16_NAJAT	Cardiotoxin I-like P-15 precursor	0.01	-	nuc	0	Secreted protein				81
Q91137 UniProt NPD GO	CXHL_NAJAT	Cardiotoxin V-like precursor	0.01	-	nuc	0	Secreted protein				83
Q06544 UniProt NPD GO	CYSP3_OSTOS	Cathepsin B-like cysteine proteinase 3 (EC 3.4.22.-) (Fragment)	0.01	-	cyt	0					174
P43507 UniProt NPD GO	CPR3_CAEEL	Cathepsin B-like cysteine proteinase 3 precursor (EC 3.4.22.-) (Cysteine protease-related 3)	0.01	-	exc	0					370
P43509 UniProt NPD GO	CPR5_CAEEL	Cathepsin B-like cysteine proteinase 5 precursor (EC 3.4.22.-) (Cysteine protease-related 5)	0.01	-	vac	0					344
O60911 UniProt NPD GO	CATL2_HUMAN	Cathepsin L2 precursor (EC 3.4.22.43) (Cathepsin V) (Cathepsin U)	0.01	-	exc	0	Lysosome (Potential)		603308	1FH0	334
Q8BM88 UniProt NPD GO	CATO_MOUSE	Cathepsin O precursor (EC 3.4.22.42)	0.01	-	exc	0					312
P05689 UniProt NPD GO	CATZ_BOVIN	Cathepsin Z (EC 3.4.22.-) (Fragment)	0.01	-	cyt	0					73
P20645 UniProt NPD GO	MPRD_HUMAN	Cation-dependent mannose-6-phosphate receptor precursor (CD Man-6-P receptor) (CD-MPR) (46 kDa manno ...	0.01	-	end	1	Lysosome; lysosomal membrane; single-pass type I membrane protein	cell surface [IEP] endosome [IDA] integral to plasma membrane [TAS]	154540		277
P24668 UniProt NPD GO	MPRD_MOUSE	Cation-dependent mannose-6-phosphate receptor precursor (CD Man-6-P receptor) (CD-MPR) (46 kDa manno ...	0.01	-	end	1	Lysosome; lysosomal membrane; single-pass type I membrane protein	late endosome [IDA]			278
Q2QLG6 UniProt NPD GO	CAV1_CALJA	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q2QLC1 UniProt NPD GO	CAV1_CALMO	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q2IBF0 UniProt NPD GO	CAV1_GORGO	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q2QLB0 UniProt NPD GO	CAV1_HORSE	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q03135 UniProt NPD GO	CAV1_HUMAN	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side. Membrane protein of ...	caveolar membrane [IDA] endoplasmic reticulum [IDA] Golgi membrane [IDA] integral to plasma membrane [TAS] lipid raft [IDA]	601047		177
P49817 UniProt NPD GO	CAV1_MOUSE	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [ISS] endoplasmic reticulum [ISS] Golgi membrane [ISS] integral to membrane of membrane fraction [IDA] integral to plasma membrane [IDA] lipid raft [IDA] perinuclear region [IDA] plasma membrane [IDA]			178
Q2QLH7 UniProt NPD GO	CAV1_OTOGA	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q2QLF2 UniProt NPD GO	CAV1_PANTR	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q6RVA9 UniProt NPD GO	CAV1_PIG	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [ISS]			178
Q2IBD7 UniProt NPD GO	CAV1_PONPY	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
P41350 UniProt NPD GO	CAV1_RAT	Caveolin-1	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [ISS] integral to membrane [TAS]			178
P33724 UniProt NPD GO	CAV1_CANFA	Caveolin-1 (Vesicular integral-membrane protein VIP21)	0.01	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side. Membrane protein of ...	caveolar membrane [IDA]			178
O46550 UniProt NPD GO	CAV2_CANFA	Caveolin-2	0.01	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q2QLD3 UniProt NPD GO	CAV2_CARPS	Caveolin-2	0.01	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q2QL80 UniProt NPD GO	CAV2_DIDMA	Caveolin-2	0.01	-	end	2	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q2QLB1 UniProt NPD GO	CAV2_HORSE	Caveolin-2	0.01	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162

You are viewing entries 87001 to 87050 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.