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
Q13490 UniProt NPD GO	BIRC2_HUMAN	Baculoviral IAP repeat-containing protein 2 (Inhibitor of apoptosis protein 2) (HIAP2) (HIAP-2) (C-I ...	0.59	-	nuc	0	Cytoplasm (Potential)		601712	1QBH	618
Q99ML1 UniProt NPD GO	BBC3_MOUSE	Bcl-2-binding component 3 (p53 up-regulated modulator of apoptosis)	0.59	-	nuc	0	Mitochondrion. Localized to the mitochondria in order to induce cytochrome c release (By similarity) ...	mitochondrion [ISS]			193
Q9TTC5 UniProt NPD GO	BTC_BOVIN	Betacellulin precursor (BTC)	0.59	+	exc	2 *	Precursor form: Cell membrane; single-pass type I membrane protein (By similarity). Mature form: Sec ...				178
Q9NQY0 UniProt NPD GO	BIN3_HUMAN	Bridging integrator 3	0.59	-	nuc	0			606396		253
Q12980 UniProt NPD GO	U171_HUMAN	CGTHBA protein (-14 gene protein)	0.59	-	nuc	0			600928		569
P15907 UniProt NPD GO	SIAT1_HUMAN	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase (EC 2.4.99.1) (Beta-galactosi ...	0.59	-	exc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	integral to membrane [ISS]	109675		406
P49070 UniProt NPD GO	CAMLG_MOUSE	Calcium signal-modulating cyclophilin ligand (CAML)	0.59	-	nuc	0	Membrane; multi-pass membrane protein				294
Q62976 UniProt NPD GO	KCMA1_RAT	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.59	-	end	6	Cell membrane; multi-pass membrane protein. Isoform 11: Endoplasmic reticulum; endoplasmic reticulum ...				1210
Q9TTH8 UniProt NPD GO	CAN3_SHEEP	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.59	-	cyt	0	Cytoplasm				822
Q7LGC8 UniProt NPD GO	CHST3_HUMAN	Carbohydrate sulfotransferase 3 (EC 2.8.2.17) (Chondroitin 6-sulfotransferase) (Chondroitin 6-O-sulf ...	0.59	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	intrinsic to Golgi membrane [ISS]	608637		479
P52497 UniProt NPD GO	SNF1_CANAL	Carbon catabolite derepressing protein kinase (EC 2.7.11.1)	0.59	-	nuc	0	Nucleus; nuclear membrane; peripheral membrane protein (By similarity)				620
Q9ULX7 UniProt NPD GO	CAH14_HUMAN	Carbonic anhydrase 14 precursor (EC 4.2.1.1) (Carbonic anhydrase XIV) (Carbonate dehydratase XIV) (C ...	0.59	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [TAS]	604832		337
P55867 UniProt NPD GO	CAS1B_XENLA	Caspase-1-B precursor (EC 3.4.22.-) (CASP-1-B) (Interleukin-1 beta convertase homolog B) (xICE-B)	0.59	-	nuc	0	Cytoplasm (By similarity)				382
P11717 UniProt NPD GO	MPRI_HUMAN	Cation-independent mannose-6-phosphate receptor precursor (CI Man-6-P receptor) (CI-MPR) (M6PR) (Ins ...	0.59	-	cyt	1	Lysosome; lysosomal membrane; single-pass type I membrane protein	endosome [IDA] integral to plasma membrane [TAS] trans-Golgi network transport vesicle [IDA]	147280	1LF8	2491
Q3T191 UniProt NPD GO	CIDEB_BOVIN	Cell death activator CIDE-B (Cell death-inducing DFFA-like effector B)	0.59	-	nuc	0					219
P32457 UniProt NPD GO	CDC3_YEAST	Cell division control protein 3	0.59	-	nuc	0	Membrane; peripheral membrane protein. Bud neck. Present at the bud neck during cell division. Proba ...	mating projection base [IDA] prospore membrane [TAS] septin ring (sensu Saccharomyces) [TAS] spore wall (sensu Fungi) [TAS]			520
Q9Y704 UniProt NPD GO	MOK14_SCHPO	Cell wall alpha-1,3-glucan synthase mok14 (EC 2.4.1.183)	0.59	-	end	13 *					1369
P38313 UniProt NPD GO	AME1_YEAST	Central kinetochore subunit AME1 (Associated with microtubules and essential protein 1)	0.59	-	nuc	0	Nucleus. Associated with kinetochores	COMA complex [IDA] kinetochore [IDA] spindle pole body [NAS]			324
O94494 UniProt NPD GO	SIM4_SCHPO	Centromere protein sim4 (Silencing in the middle of the centromere protein 4)	0.59	-	nuc	0	Nucleus. Centromeric. Associates with the central core region of the centromere	Mis6-Sim4 complex [TAS]			277
P52763 UniProt NPD GO	RR18_PINTH	Chloroplast 30S ribosomal protein S18	0.59	-	nuc	0	Plastid; chloroplast				96
P69634 UniProt NPD GO	RR4_ARUJA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.59	-	mit	0	Plastid; chloroplast				196
P69649 UniProt NPD GO	RR4_PHYFL	Chloroplast 30S ribosomal protein S4 (Fragment)	0.59	-	mit	0	Plastid; chloroplast				196
Q71L33 UniProt NPD GO	RR7_CYCRE	Chloroplast 30S ribosomal protein S7	0.59	-	nuc	0	Plastid; chloroplast				156
Q2MI65 UniProt NPD GO	RR8_LYCES	Chloroplast 30S ribosomal protein S8	0.59	-	nuc	0	Plastid; chloroplast				134
Q3C1M0 UniProt NPD GO	RR8_NICSY	Chloroplast 30S ribosomal protein S8	0.59	-	nuc	0	Plastid; chloroplast				134
Q2VEE5 UniProt NPD GO	RR8_SOLTU	Chloroplast 30S ribosomal protein S8	0.59	-	nuc	0	Plastid; chloroplast				134
P06363 UniProt NPD GO	RR8_TOBAC	Chloroplast 30S ribosomal protein S8	0.59	-	nuc	0	Plastid; chloroplast				134
Q49KV9 UniProt NPD GO	RK22_EUCGG	Chloroplast 50S ribosomal protein L22	0.59	-	nuc	0	Plastid; chloroplast				160
O19894 UniProt NPD GO	RK32_CYACA	Chloroplast 50S ribosomal protein L32	0.59	-	nuc	0	Plastid; chloroplast				52
Q9TLR9 UniProt NPD GO	RK35_CYACA	Chloroplast 50S ribosomal protein L35	0.59	-	nuc	0	Plastid; chloroplast				64
P49567 UniProt NPD GO	RK35_ODOSI	Chloroplast 50S ribosomal protein L35	0.59	-	nuc	0	Plastid; chloroplast				64
P32238 UniProt NPD GO	CCKAR_HUMAN	Cholecystokinin type A receptor (CCK-A receptor) (CCK-AR) (Cholecystokinin-1 receptor) (CCK1-R)	0.59	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	118444	1PB2	428
O97772 UniProt NPD GO	CCKAR_RABIT	Cholecystokinin type A receptor (CCK-A receptor) (CCK-AR) (Cholecystokinin-1 receptor) (CCK1-R)	0.59	-	end	7 *	Membrane; multi-pass membrane protein				427
P19836 UniProt NPD GO	PCY1A_RAT	Choline-phosphate cytidylyltransferase A (EC 2.7.7.15) (Phosphorylcholine transferase A) (CTP:phosph ...	0.59	+	nuc	0	Cytoplasm; cytosol. Membrane; peripheral membrane protein. It can interconvert between an inactive c ...	extrinsic to membrane [NAS]		1PEI	367
Q9D0N7 UniProt NPD GO	CAF1B_MOUSE	Chromatin assembly factor 1 subunit B (CAF-1 subunit B) (Chromatin assembly factor I p60 subunit) (C ...	0.59	-	nuc	0	Nucleus (By similarity). DNA replication foci (By similarity)				572
Q06168 UniProt NPD GO	SFH1_YEAST	Chromatin structure remodeling complex protein SFH1 (SNF5 homolog 1)	0.59	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			426
P04404 UniProt NPD GO	CMGA_PIG	Chromogranin A precursor (CgA) [Contains: Pancreastatin; Parastatin; WE-14] (Fragment)	0.59	-	exc	0	Neuroendocrine and endocrine secretory granules				446
Q9XS63 UniProt NPD GO	CMGA_HORSE	Chromogranin A precursor (CgA) [Contains: Pancreastatin; WE-14]	0.59	-	exc	0	Neuroendocrine and endocrine secretory granules				448
Q5ZL34 UniProt NPD GO	CPSF6_CHICK	Cleavage and polyadenylation specificity factor 6	0.59	+	nuc	0	Nucleus (By similarity)				551
P14018 UniProt NPD GO	CLUS_COTJA	Clusterin precursor (51.5 kDa protein) [Contains: Clusterin beta chain; Clusterin alpha chain]	0.59	-	mit	0	Secreted protein				451
O43513 UniProt NPD GO	CSP9_HUMAN	Cofactor required for Sp1 transcriptional activation subunit 9 (Transcriptional coactivator CRSP33) ...	0.59	-	nuc	0	Nucleus	transcription factor complex [IDA]	605045		233
Q5ZK95 UniProt NPD GO	CCD43_CHICK	Coiled-coil domain-containing protein 43	0.59	+	nuc	0					217
Q9NX63 UniProt NPD GO	CHCH3_HUMAN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 3	0.59	-	nuc	0		mitochondrion [ISS]			227
Q8CI04 UniProt NPD GO	COG3_MOUSE	Conserved oligomeric Golgi complex component 3	0.59	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein (By similarity). Ass ...				819
P49926 UniProt NPD GO	CRF_CANFA	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.59	-	mit	0	Secreted protein				196
P87352 UniProt NPD GO	COLI_ACITR	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Gamma-melanotropin- ...	0.59	-	exc	0					263
Q13616 UniProt NPD GO	CUL1_HUMAN	Cullin-1 (CUL-1)	0.59	-	cyt	0			603134	1U6G	776
Q9WTX6 UniProt NPD GO	CUL1_MOUSE	Cullin-1 (CUL-1)	0.59	-	cyt	0		SCF ubiquitin ligase complex [IDA]			776
Q5R4G6 UniProt NPD GO	CUL1_PONPY	Cullin-1 (CUL-1)	0.59	-	cyt	0					776
Q06507 UniProt NPD GO	ATF4_MOUSE	Cyclic AMP-dependent transcription factor ATF-4 (C/EBP-related ATF) (C/ATF) (TAXREB67 homolog)	0.59	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IC]			349

You are viewing entries 19451 to 19500 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.