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
Q9QXP3 UniProt NPD GO	HMGA1_CRIGR	High mobility group protein HMG-I/HMG-Y (HMG-I(Y)) (High mobility group AT-hook protein 1) (High mob ...	0.58	+	nuc	0	Nucleus				106
P26586 UniProt NPD GO	HMGL_TRYBR	High mobility group protein homolog TDP-1	0.58	-	nuc	0					271
P47808 UniProt NPD GO	MYSH_ACACA	High molecular weight form of myosin-1 (High molecular weight form of myosin I) (HMWMI)	0.58	-	cyt	0					1577
Q05733 UniProt NPD GO	DCHS_DROME	Histidine decarboxylase (EC 4.1.1.22) (HDC)	0.58	-	nuc	0					847
P40267 UniProt NPD GO	H1_LYCPN	Histone H1	0.58	-	nuc	0	Nucleus				202
P0C1H3 UniProt NPD GO	H2B1_CHICK	Histone H2B 1/2/3/4/6 (H2B I) (H2B II) (H2B III) (H2B IV) (H2B VI)	0.58	+	nuc	0	Nucleus			2HIO	125
Q00729 UniProt NPD GO	H2B1A_RAT	Histone H2B type 1-A (Histone H2B, testis) (Testis-specific histone H2B)	0.58	-	nuc	0	Nucleus				126
P06899 UniProt NPD GO	H2B1J_HUMAN	Histone H2B type 1-J (H2B.r) (H2B/r) (H2B.1)	0.58	+	nuc	0	Nucleus	nucleosome [NAS]			125
Q8CGP1 UniProt NPD GO	H2B1K_MOUSE	Histone H2B type 1-K	0.58	+	nuc	0	Nucleus				125
Q99880 UniProt NPD GO	H2B1L_HUMAN	Histone H2B type 1-L (H2B.c) (H2B/c)	0.58	+	nuc	0	Nucleus	nucleosome [NAS]	602800		125
Q2UMQ5 UniProt NPD GO	ESA1_ASPOR	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.58	-	nuc	0	Nucleus (By similarity)				506
Q6BU95 UniProt NPD GO	ESA1_DEBHA	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.58	-	nuc	0	Nucleus (By similarity)				521
Q7S7N3 UniProt NPD GO	HAT2_NEUCR	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				564
Q02959 UniProt NPD GO	HOS3_YEAST	Histone deacetylase HOS3	0.58	-	nuc	0		bud neck [IDA] cytoplasm [IDA] nucleus [IDA]			697
Q24255 UniProt NPD GO	BARH1_DROME	Homeobox protein B-H1 (Homeobox protein BarH1)	0.58	+	nuc	0	Nucleus (Probable)	nucleus [NAS]			544
Q90229 UniProt NPD GO	DLX3_AMBME	Homeobox protein DLX-3	0.58	+	nuc	0	Nucleus (Potential)				280
O60479 UniProt NPD GO	DLX3_HUMAN	Homeobox protein DLX-3	0.58	+	nuc	0	Nucleus (Potential)		600525		287
P53770 UniProt NPD GO	DLX3_NOTVI	Homeobox protein DLX-3 (Box-4) (NVHBOX-4)	0.58	+	nuc	0	Nucleus (Potential)				273
Q92988 UniProt NPD GO	DLX4_HUMAN	Homeobox protein DLX-4 (DLX-7) (DLX-8) (Beta protein 1)	0.58	+	nuc	0	Nucleus (Potential)		601911		240
P42585 UniProt NPD GO	HBX3_ECHGR	Homeobox protein EgHBX3 (Fragment)	0.58	-	mit	0	Nucleus (Probable)				167
Q9PWL6 UniProt NPD GO	HXA9A_BRARE	Homeobox protein Hox-A9a (Hoxx9)	0.58	+	nuc	0	Nucleus (By similarity)				250
P23813 UniProt NPD GO	HXD11_MOUSE	Homeobox protein Hox-D11 (Hox-4.6) (Hox-5.5)	0.58	+	nuc	0	Nucleus				323
P31249 UniProt NPD GO	HXD3_HUMAN	Homeobox protein Hox-D3 (Hox-4A)	0.58	+	nuc	0	Nucleus		142980		416
P18867 UniProt NPD GO	HXD3_RAT	Homeobox protein Hox-D3 (R6) (Fragment)	0.58	+	mit	0	Nucleus				114
P56669 UniProt NPD GO	HLG3_MAIZE	Homeobox protein liguleless 3 (Fragment)	0.58	+	nuc	0	Nucleus (Probable)				85
Q93899 UniProt NPD GO	VAB7_CAEEL	Homeobox protein vab-7	0.58	+	nuc	0	Nucleus				247
Q5DUY3 UniProt NPD GO	RL14H_NYCOV	Hydrogenosomal 60S ribosomal protein L14	0.58	-	mit	0	Hydrogenosome				133
P40895 UniProt NPD GO	YJV5_YEAST	Hypothetical 13.9 kDa protein in HXT11-HXT8 intergenic region	0.58	-	nuc	0					119
P35725 UniProt NPD GO	YKG3_YEAST	Hypothetical 19.0 kDa protein in MNR2-MSN4 intergenic region	0.58	-	nuc	1 *		Golgi apparatus [IDA]			167
P51335 UniProt NPD GO	YCXH_PORPU	Hypothetical 43.4 kDa protein in rpl9-rpl11 intergenic region (ORF382)	0.58	-	nuc	0	Plastid; chloroplast				382
P51189 UniProt NPD GO	YCF46_PORPU	Hypothetical 56.0 kDa protein ycf46 (ORF491)	0.58	-	mit	0	Plastid; chloroplast				491
Q11192 UniProt NPD GO	YX21_CAEEL	Hypothetical protein C04E7.1	0.58	-	nuc	0					113
Q10443 UniProt NPD GO	YDEA_SCHPO	Hypothetical protein C12B10.10 in chromosome I	0.58	-	nuc	0					419
Q10486 UniProt NPD GO	YDFF_SCHPO	Hypothetical protein C17C9.15c in chromosome I	0.58	-	nuc	0					94
Q09237 UniProt NPD GO	YQ82_CAEEL	Hypothetical protein C18H9.2	0.58	-	nuc	0					128
Q09773 UniProt NPD GO	YA84_SCHPO	Hypothetical protein C22F3.04 in chromosome I	0.58	-	end	0	Membrane; multi-pass membrane protein (Potential)				1428
Q9P6S3 UniProt NPD GO	YNL4_SCHPO	Hypothetical protein C27.04 in chromosome II	0.58	-	nuc	0					1052
Q8STA9 UniProt NPD GO	Y5G8_ENCCU	Hypothetical protein ECU05_1680/ECU11_0050	0.58	+	nuc	0					612
Q8STZ1 UniProt NPD GO	YBK9_ENCCU	Hypothetical protein ECU11_2090	0.58	+	cyt	0					634
Q09391 UniProt NPD GO	YR46_CAEEL	Hypothetical protein F47D12.6	0.58	-	nuc	1 *					100
P34454 UniProt NPD GO	YMA9_CAEEL	Hypothetical protein F54F2.9	0.58	-	exc	1 *	Nucleus; nuclear membrane; single-pass membrane protein (Potential)				299
Q21276 UniProt NPD GO	YZVL_CAEEL	Hypothetical protein K07C5.4 in chromosome V	0.58	+	cyt	0					486
P34621 UniProt NPD GO	YO85_CAEEL	Hypothetical protein ZK1236.5	0.58	-	nuc	0					148
P34627 UniProt NPD GO	YOJ4_CAEEL	Hypothetical protein ZK353.4	0.58	-	nuc	1 *					305
P52947 UniProt NPD GO	IPF1_RAT	Insulin promoter factor 1 (IPF-1) (Islet/duodenum homeobox 1) (IDX-1) (Somatostatin-transactivating ...	0.58	+	nuc	0	Nucleus				283
Q95222 UniProt NPD GO	IGF1_RABIT	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.58	-	exc	0	Secreted protein				143
P01570 UniProt NPD GO	IFN14_HUMAN	Interferon alpha-14 precursor (Interferon alpha-H) (LeIF H) (Interferon lambda-2-H)	0.58	-	mit	0	Secreted protein		147579		189
P49878 UniProt NPD GO	IFNAH_BOVIN	Interferon alpha-H precursor	0.58	-	mit	1 *	Secreted protein				189
O35664 UniProt NPD GO	INAR2_MOUSE	Interferon-alpha/beta receptor beta chain precursor (IFN-alpha-REC) (Type I interferon receptor) (IF ...	0.58	-	end	0	Membrane; single-pass type I membrane protein (Potential)	extracellular space [IDA] integral to membrane [TAS]			513
Q95207 UniProt NPD GO	INAR2_SHEEP	Interferon-alpha/beta receptor beta chain precursor (IFN-alpha-REC) (Type I interferon receptor) (IF ...	0.58	-	nuc	1 *	Membrane; single-pass type I membrane protein				536

You are viewing entries 20201 to 20250 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.