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
Q96398 UniProt NPD GO	CHRC_CUCSA	Chromoplast-specific carotenoid-associated protein, chloroplast precursor	0.12	-	mit	0	Plastid; chloroplast				322
Q9BSN7 UniProt NPD GO	CLP24_HUMAN	Claudin-like protein 24	0.12	-	end	4 *	Cell membrane; cell-cell junction; adherens junction; multi-pass membrane protein. Co-localizes with ...				226
Q9LKF9 UniProt NPD GO	CPSF2_ARATH	Cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.12	-	cyt	0	Nucleus (Potential)				739
Q652P4 UniProt NPD GO	CPSF2_ORYSA	Cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.12	-	nuc	0	Nucleus (By similarity)				738
Q2HJ57 UniProt NPD GO	COTL1_BOVIN	Coactosin-like protein	0.12	-	cyt	0					141
P15566 UniProt NPD GO	COAG_TACGI	Coagulogen [Contains: Coagulin chain A; Peptide C; Coagulin chain B]	0.12	-	cyt	0	Secreted protein				175
P35605 UniProt NPD GO	COPB2_BOVIN	Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP) (p102)	0.12	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			905
O55029 UniProt NPD GO	COPB2_MOUSE	Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP) (p102)	0.12	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	Golgi apparatus [IDA]			905
O35142 UniProt NPD GO	COPB2_RAT	Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP) (p102)	0.12	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	Golgi membrane [IDA]			904
P12247 UniProt NPD GO	CO3_RABIT	Complement C3 alpha chain (Fragment)	0.12	-	mit	0					726
P01032 UniProt NPD GO	CO5_PIG	Complement C5a anaphylatoxin	0.12	-	nuc	0				1C5A	74
P34090 UniProt NPD GO	CMF_DICDI	Conditioned medium factor (CMF) (Density-sensing factor)	0.12	-	mit	0					571
Q00945 UniProt NPD GO	CONO_LYMST	Conopressin/neurophysin precursor [Contains: Lys-conopressin G; Neurophysin]	0.12	-	nuc	0	Secreted protein				155
P69766 UniProt NPD GO	CX5B_CONVC	Conotoxin vc5c precursor (Conotoxin Vc5.2) (Fragment)	0.12	-	exc	0	Secreted protein				54
P00567 UniProt NPD GO	KCRB_RABIT	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.12	-	nuc	0	Cytoplasm				381
Q6HAA2 UniProt NPD GO	CTSP2_CRODU	Crotasin precursor	0.12	-	exc	0	Secreted protein				63
P08124 UniProt NPD GO	COL1_CAEEL	Cuticle collagen 1 precursor (Protein squat-3) (Protein dumpy-15)	0.12	-	nuc	1 *		extracellular region [NAS]			296
P18833 UniProt NPD GO	COL8_CAEEL	Cuticle collagen 8 precursor	0.12	-	nuc	0					282
P17657 UniProt NPD GO	DPY13_CAEEL	Cuticle collagen dpy-13 (Protein dumpy-13)	0.12	-	nuc	1 *					302
P82121 UniProt NPD GO	CUO8_BLACR	Cuticle protein 8 (BcNCP21.1)	0.12	-	nuc	0					195
P46794 UniProt NPD GO	CBS_DICDI	Cystathionine beta-synthase (EC 4.2.1.22) (Serine sulfhydrase) (Beta-thionase)	0.12	-	cyt	0					497
P46102 UniProt NPD GO	CYSP_PLAVN	Cysteine proteinase precursor (EC 3.4.22.-)	0.12	-	mit	1 *					506
P57757 UniProt NPD GO	CTNS_MOUSE	Cystinosin	0.12	-	end	7	Lysosome; lysosomal membrane; multi-pass membrane protein				367
P56389 UniProt NPD GO	CDD_MOUSE	Cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.12	-	cyt	0		cytosol [ISS] extracellular region [ISS]		1ZAB	146
Q2XV99 UniProt NPD GO	CP11A_MACFA	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.12	-	cyt	0	Mitochondrion (By similarity)				521
Q9GMC8 UniProt NPD GO	CP17A_FELCA	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.12	-	end	0					508
P19098 UniProt NPD GO	CP19A_CHICK	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.12	-	end	2 *	Membrane; peripheral membrane protein				507
Q92039 UniProt NPD GO	CP1A1_CHACA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.12	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
Q29478 UniProt NPD GO	CP2CV_CAPAE	Cytochrome P450 2C31 (EC 1.14.14.1) (CYPIIC31) (Fragment)	0.12	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				284
P56657 UniProt NPD GO	CP240_MOUSE	Cytochrome P450 2C40 (EC 1.14.14.1) (CYPIIC40)	0.12	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
Q8CIM7 UniProt NPD GO	CP2DQ_MOUSE	Cytochrome P450 2D26 (EC 1.14.14.1) (CYPIID26)	0.12	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				500
Q92088 UniProt NPD GO	CP2M1_ONCMY	Cytochrome P450 2M1 (EC 1.14.14.1) (CYPIIM1) (Lauric acid omega-6-hydroxylase) (LMC1)	0.12	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				499
Q9HB55 UniProt NPD GO	CP343_HUMAN	Cytochrome P450 3A43 (EC 1.14.14.1)	0.12	-	cyt	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]	606534		503
Q12573 UniProt NPD GO	CP52W_CANAP	Cytochrome P450 52E2 (EC 1.14.14.-) (CYPLIIE2)	0.12	-	mit	1 *					519
P58045 UniProt NPD GO	C71AE_ARATH	Cytochrome P450 71A14 (EC 1.14.-.-)	0.12	-	end	0					497
Q9FH66 UniProt NPD GO	C71AG_ARATH	Cytochrome P450 71A16 (EC 1.14.-.-)	0.12	-	nuc	1 *					497
P48417 UniProt NPD GO	CP74_LINUS	Cytochrome P450 74A, chloroplast precursor (EC 4.2.1.92) (Allene oxide synthase) (Hydroperoxide dehy ...	0.12	-	mit	0	Plastid; chloroplast (Probable)				536
Q7Y1V5 UniProt NPD GO	C78AB_ORYSA	Cytochrome P450 78A11 (EC 1.14.-.-) (Protein PLASTOCHRON1)	0.12	-	vac	1 *					555
P98188 UniProt NPD GO	C94A2_VICSA	Cytochrome P450 94A2 (EC 1.14.-.-) (P450-dependent fatty acid omega-hydroxylase)	0.12	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				513
Q9N2H0 UniProt NPD GO	CY24A_TURTR	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.12	-	end	4 *					191
Q8MAV7 UniProt NPD GO	PSBE_CUSGR	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.12	-	mit	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				83
P29380 UniProt NPD GO	CYC1_ARATH	Cytochrome c	0.12	-	cyt	0	Mitochondrion; mitochondrial matrix				112
P00017 UniProt NPD GO	CYC_APTPA	Cytochrome c	0.12	-	nuc	0	Mitochondrion; mitochondrial matrix				104
Q753F4 UniProt NPD GO	CYC_ASHGO	Cytochrome c	0.12	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				110
P00029 UniProt NPD GO	CYC_ASTRU	Cytochrome c	0.12	-	cyt	0	Mitochondrion; mitochondrial matrix				103
P19681 UniProt NPD GO	CYC_DEBOC	Cytochrome c	0.12	-	nuc	0	Mitochondrion; mitochondrial matrix				109
Q6C9Q0 UniProt NPD GO	CYC_YARLI	Cytochrome c	0.12	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				107
P39103 UniProt NPD GO	COX14_YEAST	Cytochrome c oxidase assembly protein COX14	0.12	-	mit	1 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	extrinsic to membrane [IDA] integral to membrane [IDA] mitochondrial envelope [IDA] mitochondrial inner membrane [IDA] mitochondrial matrix [IDA]			70
P09669 UniProt NPD GO	COX6C_HUMAN	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.12	-	mit	1 *	Mitochondrion; mitochondrial inner membrane		124090		75
O99041 UniProt NPD GO	COX1_COLPO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.12	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514

You are viewing entries 61001 to 61050 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.