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
P35458 UniProt NPD GO	DYNA_CHICK	Dynactin-1 (150 kDa dynein-associated polypeptide) (DP-150) (DAP-150) (p150-glued)	0.86	-	nuc	0	Cytoplasm				1224
O23116 UniProt NPD GO	EIL3_ARATH	ETHYLENE-INSENSITIVE3-like 3 protein	0.86	-	nuc	0	Nucleus (By similarity)			1WIJ	567
P34529 UniProt NPD GO	DCR1_CAEEL	Endoribonuclease dcr-1 (EC 3.1.26.-)	0.86	-	cyt	0					1845
P20800 UniProt NPD GO	EDN2_HUMAN	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.86	-	exc	0	Secreted protein	soluble fraction [TAS]	131241		178
Q91WL0 UniProt NPD GO	ES8L3_MOUSE	Epidermal growth factor receptor pathway substrate 8-like protein 3 (Epidermal growth factor recepto ...	0.86	-	nuc	0	Cytoplasm (By similarity)				600
Q9UPT5 UniProt NPD GO	EXOC7_HUMAN	Exocyst complex component 7 (Exocyst complex component Exo70)	0.86	+	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane; peripheral membrane protein (By similarity). Tran ...		608163		735
P32855 UniProt NPD GO	SEC8_YEAST	Exocyst complex component SEC8	0.86	-	nuc	0	Cytoplasm. 75%. Cell membrane; peripheral membrane protein. 25%	bud tip [IDA] exocyst [IPI] incipient bud site [TAS]			1065
Q5IGR6 UniProt NPD GO	EXT1C_BRARE	Exostosin-1c (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylg ...	0.86	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	integral to endoplasmic reticulum membrane [ISS]			737
Q00976 UniProt NPD GO	SPT16_KLULA	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16) (Cell divisio ...	0.86	-	nuc	0	Nucleus (By similarity)				1033
O94887 UniProt NPD GO	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain-containing protein 2 (FERM domain including RhoGEF) (FIR)	0.86	-	cyt	0		cytoplasm [IDA]			1054
Q6ZNL6 UniProt NPD GO	FGD5_HUMAN	FYVE, RhoGEF and PH domain-containing protein 5 (Zinc finger FYVE domain-containing protein 23)	0.86	+	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS] Golgi apparatus [ISS] lamellipodium [ISS] ruffle [ISS]			1462
Q69ZL1 UniProt NPD GO	FGD6_MOUSE	FYVE, RhoGEF and PH domain-containing protein 6	0.86	+	nuc	0	Cytoplasm (Probable)			1WGQ	1399
Q9HB96 UniProt NPD GO	FANCE_HUMAN	Fanconi anemia group E protein (Protein FACE)	0.86	-	nuc	0	Nucleus	nucleus [NAS]	600901		536
P20134 UniProt NPD GO	SFL1_YEAST	Flocculation suppression protein (Protein SFL1)	0.86	+	nuc	0	Nucleus (Probable)	nuclear chromosome [IPI]			766
P35632 UniProt NPD GO	AP3_ARATH	Floral homeotic protein APETALA3	0.86	-	nuc	0	Nucleus				232
Q9NU39 UniProt NPD GO	FX4L1_HUMAN	Forkhead box protein D4-like 1	0.86	-	nuc	0	Nucleus (By similarity)				408
Q922I5 UniProt NPD GO	FOXI1_MOUSE	Forkhead box protein I1	0.86	+	nuc	0	Nucleus				345
P20437 UniProt NPD GO	CG11_YEAST	G1/S-specific cyclin CLN1	0.86	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			546
Q6GYP7 UniProt NPD GO	GRIPE_MOUSE	GTPase-activating RapGAP domain-like 1 (GAP-related-interacting partner to E12) (GRIPE) (Tuberin-lik ...	0.86	-	nuc	0	Cytoplasm. Nucleus. Translocated to the nucleus, when associated with TCF3/E12	cytoplasm [IDA] nucleus [IDA]			2035
Q9QYB5 UniProt NPD GO	ADDG_MOUSE	Gamma-adducin (Adducin-like protein 70)	0.86	+	nuc	0		cytoskeleton [IDA] membrane [IDA]			706
Q9D1C9 UniProt NPD GO	ZG14_MOUSE	Gastric cancer antigen Zg14 homolog	0.86	-	nuc	0					280
P07261 UniProt NPD GO	GCR1_YEAST	Glycolytic genes transcriptional activator GCR1	0.86	+	nuc	0	Nucleus	nucleus [IC]			785
P02895 UniProt NPD GO	GBP_PLAFG	Glycophorin-binding protein (GBP-130)	0.86	-	nuc	1 *	Erythrocyte cytoplasm of schizonts. Released into the culture supernatant at the time of schizont ru ...				774
Q9Z1E9 UniProt NPD GO	GSLG1_CRIGR	Golgi apparatus protein 1 precursor (Golgi sialoglycoprotein MG-160) (E-selectin ligand 1) (ESL-1) ( ...	0.86	-	end	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein (By similarity)				1160
Q8S8N9 UniProt NPD GO	GOGA5_ARATH	Golgin-84	0.86	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				707
P90970 UniProt NPD GO	GOGA5_CAEEL	Golgin-84	0.86	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi apparatus [ISS]			530
P12611 UniProt NPD GO	WHI2_YEAST	Growth regulation protein	0.86	-	nuc	0					486
P20354 UniProt NPD GO	GNAS_DROME	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.86	-	nuc	0		plasma membrane [IDA]			385
Q9I9L0 UniProt NPD GO	HEY2_BRARE	Hairy/enhancer-of-split related with YRPW motif 2 (Protein gridlock)	0.86	-	nuc	0	Nucleus (Probable)	nucleus [IC]			324
P32828 UniProt NPD GO	HEX3_YEAST	Hexose metabolism-related protein HEX3	0.86	+	nuc	0					619
P02256 UniProt NPD GO	H1_PARAN	Histone H1, gonadal	0.86	+	nuc	0	Nucleus				248
P06513 UniProt NPD GO	H5_CAIMO	Histone H5	0.86	+	nuc	0	Nucleus				193
Q8WUI4 UniProt NPD GO	HDAC7_HUMAN	Histone deacetylase 7a (HD7a)	0.86	-	nuc	0	Nucleus. Cytoplasm. In the nucleus, it associates with distinct subnuclear dot-like structures. Shut ...	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]	606542		952
Q04089 UniProt NPD GO	DOT1_YEAST	Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) (Histone H3-K79 methyltransf ...	0.86	-	nuc	0	Nucleus (Probable)	nucleus [IDA]		1U2Z	582
P22574 UniProt NPD GO	HXB4A_BRARE	Homeobox protein Hox-B4a (Hox-B4) (Zf-13)	0.86	+	nuc	0	Nucleus				246
Q9YGS6 UniProt NPD GO	HXC9A_BRARE	Homeobox protein Hox-C9a (Hox-C9)	0.86	+	nuc	0	Nucleus (By similarity)				260
Q9M6D9 UniProt NPD GO	STM_BRAOL	Homeobox protein Shootmeristemless	0.86	+	nuc	0	Nucleus (Probable)				383
Q8IUE0 UniProt NPD GO	TF2LY_HUMAN	Homeobox protein TGIF2LY (TGFB-induced factor 2-like protein, Y-linked) (TGF(beta)induced transcript ...	0.86	-	nuc	0	Nucleus (By similarity)		400025		185
Q19503 UniProt NPD GO	HM40_CAEEL	Homeobox protein ceh-40	0.86	-	nuc	0	Nucleus (Probable)				329
P52729 UniProt NPD GO	HME2A_XENLA	Homeobox protein engrailed-2-A (En-2A) (EN2 1.4)	0.86	+	nuc	0	Nucleus (Potential)				265
P52730 UniProt NPD GO	HME2B_XENLA	Homeobox protein engrailed-2-B (En-2B) (EN2 MABEN)	0.86	+	nuc	0	Nucleus (Potential)				265
O04134 UniProt NPD GO	KNAP1_MALDO	Homeobox protein knotted-1-like 1 (KNAP1)	0.86	-	nuc	0	Nucleus (Probable)				398
O04136 UniProt NPD GO	KNAP3_MALDO	Homeobox protein knotted-1-like 3 (KNAP3)	0.86	+	nuc	0	Nucleus (Probable)				427
O09113 UniProt NPD GO	OTP_MOUSE	Homeobox protein orthopedia	0.86	+	nuc	0	Nucleus (By similarity)				325
P46665 UniProt NPD GO	HAT14_ARATH	Homeobox-leucine zipper protein HAT14 (HD-ZIP protein 14)	0.86	+	nuc	0	Nucleus (Potential)				336
Q86Z02 UniProt NPD GO	HIPK1_HUMAN	Homeodomain-interacting protein kinase 1 (EC 2.7.11.1)	0.86	-	nuc	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity)		608003		1210
Q9QZR5 UniProt NPD GO	HIPK2_MOUSE	Homeodomain-interacting protein kinase 2 (EC 2.7.11.1) (Nuclear body-associated kinase 1) (Sialophor ...	0.86	-	nuc	0	Nucleus. Concentrated in PML/POD/ND10 nuclear bodies. Isoform 2 seems to be both nuclear and cytopla ...	cytoplasm [IDA] nucleus [IDA] PML body [TAS]			1196
Q00547 UniProt NPD GO	HMMR_MOUSE	Hyaluronan mediated motility receptor (Intracellular hyaluronic acid-binding protein) (Receptor for ...	0.86	-	nuc	0	Cell surface. Cytoplasm				794
P47170 UniProt NPD GO	YJ9G_YEAST	Hypothetical 182.0 kDa protein in NMD5-HOM6 intergenic region	0.86	-	mit	0		vacuolar membrane (sensu Fungi) [IDA]			1584
P53891 UniProt NPD GO	YNQ5_YEAST	Hypothetical 46.2 kDa protein in SKO1-RPL44A intergenic region	0.86	-	nuc	0					406

You are viewing entries 6051 to 6100 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.