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
Q3V501 UniProt NPD GO	RR11_ACOCL	Chloroplast 30S ribosomal protein S11	0.31	-	mit	0	Plastid; chloroplast				138
Q7YJU5 UniProt NPD GO	RR11_CALFE	Chloroplast 30S ribosomal protein S11	0.31	-	mit	0	Plastid; chloroplast				138
Q9TL27 UniProt NPD GO	RR11_NEPOL	Chloroplast 30S ribosomal protein S11	0.31	-	nuc	0	Plastid; chloroplast				130
P25875 UniProt NPD GO	RR16_HORVU	Chloroplast 30S ribosomal protein S16	0.31	-	mit	0	Plastid; chloroplast				85
Q9MUR5 UniProt NPD GO	RR16_MESVI	Chloroplast 30S ribosomal protein S16	0.31	-	mit	0	Plastid; chloroplast				84
Q6EW66 UniProt NPD GO	RR16_NYMAL	Chloroplast 30S ribosomal protein S16	0.31	-	mit	0	Plastid; chloroplast				86
Q2L946 UniProt NPD GO	RR3_GOSHI	Chloroplast 30S ribosomal protein S3	0.31	-	mit	0	Plastid; chloroplast				218
P41635 UniProt NPD GO	RR3_PINTH	Chloroplast 30S ribosomal protein S3	0.31	-	mit	0	Plastid; chloroplast				217
P19459 UniProt NPD GO	RR9_GUITH	Chloroplast 30S ribosomal protein S9	0.31	-	nuc	0	Plastid; chloroplast				134
P07815 UniProt NPD GO	RK36_PEA	Chloroplast 50S ribosomal protein L36	0.31	-	mit	0	Plastid; chloroplast				37
Q6YXR1 UniProt NPD GO	CEMA_PHYPA	Chloroplast envelope membrane protein	0.31	-	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				439
P09240 UniProt NPD GO	CCKN_MOUSE	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 33 (CCK33); Cholecystokinin 12 (CCK12); ...	0.31	-	exc	0		axon [IDA]			115
Q9BU40 UniProt NPD GO	CRDL1_HUMAN	Chordin-like protein 1 precursor (Neuralin) (Ventroptin)	0.31	-	exc	0	Secreted protein (Potential)				450
P57720 UniProt NPD GO	AROC_ARATH	Chorismate synthase, chloroplast precursor (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phosphol ...	0.31	-	nuc	0	Plastid; chloroplast (By similarity)				436
P33716 UniProt NPD GO	CMGA_STRCA	Chromogranin A (Fragments)	0.31	-	nuc	0					104
P30388 UniProt NPD GO	1OKO_GORGO	Class I histocompatibility antigen, GOGO-OKO alpha chain precursor	0.31	-	end	1	Membrane; single-pass type I membrane protein				362
Q96B33 UniProt NPD GO	CLD23_HUMAN	Claudin-23	0.31	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]	609203		292
Q28104 UniProt NPD GO	COPE_BOVIN	Coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.31	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			307
Q60445 UniProt NPD GO	COPE_CRIGR	Coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP) (LDLF)	0.31	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				307
P53600 UniProt NPD GO	COPZ_YEAST	Coatomer subunit zeta (Zeta-coat protein) (Zeta-COP)	0.31	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IMP]			189
P45695 UniProt NPD GO	COF1A_XENLA	Cofilin-1-A	0.31	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				167
P45591 UniProt NPD GO	COF2_MOUSE	Cofilin-2 (Cofilin, muscle isoform)	0.31	+	cyt	0	Nucleus. Cytoplasm				166
Q9HA90 UniProt NPD GO	CCD48_HUMAN	Coiled-coil domain-containing protein 48	0.31	-	cyt	0					161
Q9D2R6 UniProt NPD GO	CCD56_MOUSE	Coiled-coil domain-containing protein 56	0.31	-	nuc	1		mitochondrion [IDA]			108
Q4R9C9 UniProt NPD GO	CCD70_MACFA	Coiled-coil domain-containing protein 70 precursor	0.31	-	mit	0	Secreted protein (Potential)				232
Q9CQP3 UniProt NPD GO	CHCH5_MOUSE	Coiled-coil-helix-coiled-coil-helix domain-containing protein 5	0.31	-	nuc	0					110
P02452 UniProt NPD GO	CO1A1_HUMAN	Collagen alpha-1(I) chain precursor	0.31	-	exc	0			120150	1Q7D	1464
P02458 UniProt NPD GO	CO2A1_HUMAN	Collagen alpha-1(II) chain precursor [Contains: Chondrocalcin]	0.31	-	exc	0			108300	2SEB	1418
P13944 UniProt NPD GO	COCA1_CHICK	Collagen alpha-1(XII) chain precursor (Fibrochimerin)	0.31	-	mit	0					3124
P06683 UniProt NPD GO	CO9_MOUSE	Complement component C9 precursor	0.31	-	exc	0	Secreted protein				548
P08174 UniProt NPD GO	DAF_HUMAN	Complement decay-accelerating factor precursor (CD55 antigen)	0.31	-	exc	0	Isoform 2: Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS] soluble fraction [TAS]	125240	2C8I	381
P51160 UniProt NPD GO	PDE6C_HUMAN	Cone cGMP-specific 3',5'-cyclic phosphodiesterase alpha'-subunit (EC 3.1.4.35) (cGMP phosphodiestera ...	0.31	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		600827		858
P97528 UniProt NPD GO	CNTN6_RAT	Contactin-6 precursor (Neural recognition molecule NB-3)	0.31	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				1028
Q04368 UniProt NPD GO	CSI1_YEAST	Cop9 signalosome-interactor 1	0.31	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IDA]			295
Q920M5 UniProt NPD GO	CORO6_MOUSE	Coronin-6 (Clipin E)	0.31	-	nuc	0					471
O42603 UniProt NPD GO	CRFR2_XENLA	Corticotropin-releasing factor receptor 2 precursor (CRF-R 2) (CRF2) (Corticotropin-releasing hormon ...	0.31	-	end	7	Membrane; multi-pass membrane protein				413
P23401 UniProt NPD GO	RR3_CYAPA	Cyanelle 30S ribosomal protein S3	0.31	-	mit	0	Plastid; cyanelle				219
P48134 UniProt NPD GO	RR6_CYAPA	Cyanelle 30S ribosomal protein S6	0.31	-	nuc	0	Plastid; cyanelle				104
Q94AS9 UniProt NPD GO	CNGC4_ARATH	Cyclic nucleotide-gated ion channel 4 (AtCNGC4) (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.31	-	end	7	Cell membrane; multi-pass membrane protein (Potential)				694
P18606 UniProt NPD GO	CCNA1_XENLA	Cyclin-A1	0.31	-	mit	0					418
P37881 UniProt NPD GO	CCNA2_MESAU	Cyclin-A2 (Cyclin-A)	0.31	-	nuc	0					421
P51943 UniProt NPD GO	CCNA2_MOUSE	Cyclin-A2 (Cyclin-A)	0.31	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			422
P87187 UniProt NPD GO	NFS1_CANMA	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7) (tRNA-splicing protein SPL1)	0.31	+	mit	0	Mitochondrion (By similarity)				484
Q6PZ05 UniProt NPD GO	ATG4A_BOVIN	Cysteine protease ATG4A (EC 3.4.22.-) (Autophagy-related protein 4 homolog A) (Autophagy-related cys ...	0.31	-	cyt	0	Cytoplasm (Probable)				398
P43297 UniProt NPD GO	RD21A_ARATH	Cysteine proteinase RD21a precursor (EC 3.4.22.-) (RD21)	0.31	-	exc	0					462
Q8MJC8 UniProt NPD GO	CMAH_GORGO	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.31	-	nuc	0	Cytoplasm (By similarity)				600
P15150 UniProt NPD GO	C11B1_BOVIN	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.31	-	cyt	0	Mitochondrion				503
P19100 UniProt NPD GO	CP17A_PIG	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.31	-	mit	0					509
O73686 UniProt NPD GO	CP192_CARAU	Cytochrome P450 19 type 2 (EC 1.14.14.1) (Ovarian aromatase) (CYPXIXA2) (Estrogen synthetase) (P-450 ...	0.31	-	end	0	Membrane; peripheral membrane protein				518
P20853 UniProt NPD GO	CP2A7_HUMAN	Cytochrome P450 2A7 (EC 1.14.14.1) (CYPIIA7) (P450-IIA4)	0.31	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		608054		494

You are viewing entries 39301 to 39350 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.