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
O97960 UniProt NPD GO	ANDR_PAPHA	Androgen receptor (Dihydrotestosterone receptor)	0.82	+	nuc	0	Nucleus				895
Q9CZK6 UniProt NPD GO	ANKS3_MOUSE	Ankyrin repeat and SAM domain-containing protein 3	0.82	-	nuc	0					655
Q8N957 UniProt NPD GO	ANKF1_HUMAN	Ankyrin repeat and fibronectin type-III domain-containing protein 1	0.82	-	nuc	0					763
O35815 UniProt NPD GO	ATX3_RAT	Ataxin-3 (EC 3.4.22.-) (Machado-Joseph disease protein 1 homolog)	0.82	-	nuc	0	Nucleus (By similarity)				355
P54252 UniProt NPD GO	ATX3_HUMAN	Ataxin-3 (EC 3.4.22.-) (Machado-Joseph disease protein 1) (Spinocerebellar ataxia type 3 protein)	0.82	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Predominantly nuclear, but not exclusively; inner nuclear matr ...	cytoplasm [TAS] nucleoplasm [TAS]	109150	2AGA	376
Q6C315 UniProt NPD GO	ATG13_YARLI	Autophagy-related protein 13	0.82	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				715
Q6BIL4 UniProt NPD GO	ATG18_DEBHA	Autophagy-related protein 18	0.82	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				562
O42400 UniProt NPD GO	AXN_CHICK	Axin (Axis inhibition protein)	0.82	-	nuc	0	Cytoplasm (By similarity)				841
Q91Z96 UniProt NPD GO	BMP2K_MOUSE	BMP-2-inducible protein kinase (EC 2.7.11.1) (BIKe)	0.82	-	nuc	0	Nucleus	nucleus [IDA]			1138
O70445 UniProt NPD GO	BARD1_MOUSE	BRCA1-associated RING domain protein 1 (BARD-1)	0.82	-	nuc	0	Nucleus. Cytoplasm. Can translocate to the cytoplasm	BRCA1-BARD1 complex [ISS] cytoplasm [ISS] nucleus [ISS] ubiquitin ligase complex [ISS]			765
Q10337 UniProt NPD GO	BRC1_SCHPO	BRCT-containing protein 1	0.82	-	nuc	0					878
P11827 UniProt NPD GO	GLCAP_SOYBN	Beta-conglycinin, alpha' chain precursor	0.82	-	nuc	1 *	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				639
Q8UVR5 UniProt NPD GO	BAZ1A_XENLA	Bromodomain adjacent to zinc finger domain 1A (ATP-utilizing chromatin assembly and remodeling facto ...	0.82	-	nuc	0	Nucleus				627
O88379 UniProt NPD GO	BAZ1A_MOUSE	Bromodomain adjacent to zinc finger domain 1A (Cbp146) (Fragment)	0.82	-	nuc	0	Nucleus. Concentrated in pericentric heterochromatin at both interphase and metaphase	nuclear chromosome [IDA]			344
P15379 UniProt NPD GO	CD44_MOUSE	CD44 antigen precursor (Phagocytic glycoprotein 1) (PGP-1) (HUTCH-I) (Extracellular matrix receptor ...	0.82	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			778
Q9Z1X9 UniProt NPD GO	CC45L_MOUSE	CDC45-related protein (PORC-PI-1)	0.82	+	cyt	0	Nucleus				566
Q8K3M5 UniProt NPD GO	CABL2_MOUSE	CDK5 and ABL1 enzyme substrate 2 (Interactor with CDK3 2) (Ik3-2)	0.82	-	mit	0					481
P91927 UniProt NPD GO	A60DA_DROME	Calcium-binding mitochondrial protein Anon-60Da	0.82	-	nuc	1	Mitochondrion	mitochondrion [IDA]			1013
Q9H2A9 UniProt NPD GO	CHST8_HUMAN	Carbohydrate sulfotransferase 8 (EC 2.8.2.-) (N-acetylgalactosamine-4-O-sulfotransferase 1) (GalNAc- ...	0.82	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [NAS]			424
Q8WXD9 UniProt NPD GO	CSKI1_HUMAN	Caskin-1 (CASK-interacting protein 1)	0.82	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			1431
O60716 UniProt NPD GO	CTND1_HUMAN	Catenin delta-1 (p120 catenin) (p120(ctn)) (Cadherin-associated Src substrate) (CAS) (p120(cas))	0.82	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [NAS] nucleus [NAS]	601045		968
Q20932 UniProt NPD GO	BYN1_CAEEL	Cell adhesion protein byn-1	0.82	-	cyt	0					449
P67938 UniProt NPD GO	P53_BOSIN	Cellular tumor antigen p53 (Tumor suppressor p53)	0.82	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			386
P67939 UniProt NPD GO	P53_BOVIN	Cellular tumor antigen p53 (Tumor suppressor p53)	0.82	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			386
Q02732 UniProt NPD GO	CTF19_YEAST	Central kinetochore subunit CTF19 (Chromosome transmission fidelity protein 19) (Minichromosome main ...	0.82	-	nuc	0	Nucleus. Associated with kinetochores	COMA complex [IDA] nucleus [IDA]			369
P56351 UniProt NPD GO	RR2_CHLVU	Chloroplast 30S ribosomal protein S2	0.82	+	nuc	0	Plastid; chloroplast				267
Q8M9Y8 UniProt NPD GO	RK20_CHAGL	Chloroplast 50S ribosomal protein L20	0.82	-	nuc	0	Plastid; chloroplast				115
Q6EW30 UniProt NPD GO	RK20_NYMAL	Chloroplast 50S ribosomal protein L20	0.82	-	mit	0	Plastid; chloroplast				115
O54804 UniProt NPD GO	CHKA_MOUSE	Choline kinase alpha (EC 2.7.1.32) (CK) (CHETK-alpha)	0.82	-	nuc	0	Cytoplasm				453
Q01134 UniProt NPD GO	CHKA_RAT	Choline kinase alpha (EC 2.7.1.32) (CK) (CHETK-alpha)	0.82	-	nuc	0	Cytoplasm				453
Q9ULV3 UniProt NPD GO	CIZ1_HUMAN	Cip1-interacting zinc finger protein (Nuclear protein NP94)	0.82	-	nuc	0	Nucleus	nucleus [TAS]			898
Q80VN0 UniProt NPD GO	CCD37_MOUSE	Coiled-coil domain-containing protein 37	0.82	-	nuc	0					459
Q8VEG0 UniProt NPD GO	CCD71_MOUSE	Coiled-coil domain-containing protein 71	0.82	+	nuc	0					433
Q9CR92 UniProt NPD GO	CCD96_MOUSE	Coiled-coil domain-containing protein 96	0.82	-	nuc	0					584
Q96P20 UniProt NPD GO	CIAS1_HUMAN	Cold autoinflammatory syndrome 1 protein (Cryopyrin) (NACHT-, LRR- and PYD-containing protein 3) (PY ...	0.82	-	nuc	0	Cytoplasm	cytoplasm [TAS]	607115		1034
P0C0L5 UniProt NPD GO	CO4B_HUMAN	Complement C4-B precursor (Basic complement C4) [Contains: Complement C4 beta chain; Complement C4-B ...	0.82	+	mit	0			120820		1744
Q9YHY6 UniProt NPD GO	CND1_XENLA	Condensin complex subunit 1 (Chromosome-associated protein D2) (Chromosome assembly protein XCAP-D2) ...	0.82	-	cyt	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin core heterodimer [ISS] cytoplasm [ISS] nucleus [ISS]			1364
Q06156 UniProt NPD GO	CND1_YEAST	Condensin complex subunit 1 (XCAP-D2 homolog)	0.82	-	nuc	0	Nucleus. Nuclear throughout the cell cycle. During mitosis, most of the condensin complex is associa ...	nuclear condensin complex [IPI] nucleolus [IDA]			1176
P13919 UniProt NPD GO	CVCB_PEA	Convicilin precursor (Fragment)	0.82	+	end	1 *	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				386
Q9YGK5 UniProt NPD GO	COLI2_CYPCA	Corticotropin-lipotropin 2 precursor (Corticotropin-lipotropin II) (Pro-opiomelanocortin II) (POMC I ...	0.82	-	nuc	0					222
P42753 UniProt NPD GO	CCND3_ARATH	Cyclin delta-3	0.82	+	nuc	0					376
Q9JM01 UniProt NPD GO	CDKL3_RAT	Cyclin-dependent kinase-like 3 (EC 2.7.11.22) (Serine/threonine protein kinase NKIATRE)	0.82	-	nuc	0	Isoform 2: Nucleus. Isoform 2, isoform 3: Cytoplasm				593
Q07533 UniProt NPD GO	CYK3_YEAST	Cytokinesis protein 3	0.82	-	nuc	0	Cytoplasm. Bud neck. Found in association with the actin ring and the cortex at the mother-bud neck	bud neck [IDA] cytoplasm [IDA]			885
O55156 UniProt NPD GO	CYLN2_RAT	Cytoplasmic linker protein 2 (Cytoplasmic linker protein 115) (CLIP-115)	0.82	-	nuc	0	Cytoplasm (By similarity). Associated with the cytoskeleton (By similarity)	cytoplasmic microtubule [IDA] dendrite [TAS] lamellar body [TAS] microtubule associated complex [IDA]			1046
Q6BWK6 UniProt NPD GO	DAM1_DEBHA	DASH complex subunit DAM1 (Outer kinetochore protein DAM1)	0.82	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				294
P36131 UniProt NPD GO	SPC34_YEAST	DASH complex subunit SPC34 (Outer kinetochore protein SPC34) (34 kDa spindle pole component protein) ...	0.82	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle microtubule [IDA] spindle pole body [IDA]			295
P49917 UniProt NPD GO	DNL4_HUMAN	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.82	+	cyt	0	Nucleus	nucleus [TAS]	601837	1IK9	911
P54276 UniProt NPD GO	MSH6_MOUSE	DNA mismatch repair protein MSH6 (MutS-alpha 160 kDa subunit) (G/T mismatch-binding protein) (GTBP) ...	0.82	+	mit	0					1358
O93794 UniProt NPD GO	TOP2_CANGA	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.82	+	nuc	0	Nucleus (By similarity)				1406
P11388 UniProt NPD GO	TOP2A_HUMAN	DNA topoisomerase 2-alpha (EC 5.99.1.3) (DNA topoisomerase II, alpha isozyme)	0.82	+	nuc	0	Cytoplasm. Nucleus; nucleoplasm. Generally located in the nucleoplasm	nucleus [TAS]	126430	1ZXN	1531

You are viewing entries 7751 to 7800 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.