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
P87893 UniProt NPD GO	POK11_HUMAN	HERV-K_22q11.21 provirus ancestral Pol protein (HERV-K101 Pol protein) [Includes: Reverse transcript ...	0.50	-	nuc	0					254
P62688 UniProt NPD GO	GAK15_HUMAN	HERV-K_3q21.2 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K(I) Gag protein)	0.50	-	nuc	0					155
P22757 UniProt NPD GO	HE_PARLI	Hatching enzyme precursor (EC 3.4.24.12) (HE) (HEZ) (Envelysin) (Sea-urchin-hatching proteinase) [Co ...	0.50	-	exc	0					587
P22335 UniProt NPD GO	HSF24_LYCPE	Heat shock factor protein HSF24 (Heat shock transcription factor 24) (HSTF 24) (Heat stress transcri ...	0.50	-	exc	0	Nucleus				301
O44001 UniProt NPD GO	HSP90_EIMTE	Heat shock protein 90	0.50	-	cyt	0					713
P20897 UniProt NPD GO	HRT2_CRORU	Hemorrhagic metalloproteinase HT-2 (EC 3.4.24.48) (Ruberlysin) (Hemorrhagic toxin II)	0.50	-	nuc	0	Secreted protein				202
Q2QLG5 UniProt NPD GO	MET_CALJA	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.50	-	end	1	Membrane; single-pass type I membrane protein				1381
Q75ZY9 UniProt NPD GO	MET_CANFA	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.50	-	end	1	Membrane; single-pass type I membrane protein				1382
P16056 UniProt NPD GO	MET_MOUSE	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.50	-	end	1	Membrane; single-pass type I membrane protein	membrane fraction [IDA]			1379
Q2QLH6 UniProt NPD GO	MET_OTOGA	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.50	-	end	1	Membrane; single-pass type I membrane protein				1382
Q2QLE0 UniProt NPD GO	MET_PIG	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.50	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1381
Q2IBD8 UniProt NPD GO	MET_PONPY	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.50	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1390
Q91739 UniProt NPD GO	HNFAB_XENLA	Hepatocyte nuclear factor 1-alpha B (HNF-1A-B) (HNF-1-alpha B) (LFB1) (XLFB1B)	0.50	+	nuc	0	Nucleus				592
P35583 UniProt NPD GO	HNF3B_MOUSE	Hepatocyte nuclear factor 3-beta (HNF-3B) (Forkhead box protein A2)	0.50	+	nuc	0	Nucleus	nucleus [IDA]			459
P32182 UniProt NPD GO	HNF3B_RAT	Hepatocyte nuclear factor 3-beta (HNF-3B) (Forkhead box protein A2)	0.50	+	nuc	0	Nucleus				458
Q9UGV6 UniProt NPD GO	HMG1X_HUMAN	High mobility group protein 1-like 10 (HMG-1L10)	0.50	-	nuc	0	Nucleus (By similarity)	condensed chromosome [ISS]			211
Q9N2B1 UniProt NPD GO	HRH1_GORGO	Histamine H1 receptor	0.50	-	end	7 *	Membrane; multi-pass membrane protein				487
Q6B910 UniProt NPD GO	SYH_GRATL	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.50	-	nuc	0	Plastid; chloroplast				420
Q5G577 UniProt NPD GO	H2B_MAGGR	Histone H2B	0.50	-	nuc	0	Nucleus				136
P37210 UniProt NPD GO	H2B_NEUCR	Histone H2B	0.50	-	nuc	0	Nucleus				136
Q99879 UniProt NPD GO	H2B1M_HUMAN	Histone H2B type 1-M (H2B.e) (H2B/e)	0.50	+	nuc	0	Nucleus	nucleosome [NAS]	602802		125
Q64525 UniProt NPD GO	H2B2B_MOUSE	Histone H2B type 2-B (H2b 616)	0.50	+	nuc	0	Nucleus				125
Q5QNW6 UniProt NPD GO	H2B2F_HUMAN	Histone H2B type 2-F	0.50	+	nuc	0	Nucleus				125
P56518 UniProt NPD GO	HDAC1_STRPU	Histone deacetylase 1 (HD1)	0.50	-	nuc	0	Nucleus (Potential)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			576
Q8VZ17 UniProt NPD GO	SUVH6_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.50	-	nuc	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				790
P49640 UniProt NPD GO	EVX1_HUMAN	Homeobox even-skipped homolog protein 1 (EVX-1)	0.50	+	nuc	0	Nucleus		142996		407
Q91898 UniProt NPD GO	ANF1_XENLA	Homeobox protein ANF-1 (XANF-1)	0.50	+	nuc	0	Nucleus (Probable)				187
P09634 UniProt NPD GO	HXA7_RAT	Homeobox protein Hox-A7 (Hox-1.1) (R5) (Fragment)	0.50	+	nuc	0	Nucleus				105
P14157 UniProt NPD GO	HXB5_SHEEP	Homeobox protein Hox-B5 (Homeobox protein Hox-2.1) (OHox-2.1) (Fragment)	0.50	-	nuc	0	Nucleus				46
P17486 UniProt NPD GO	EGL5_CAEEL	Homeobox protein egl-5 (Homeobox protein ceh-11) (Egg-laying defective protein 5)	0.50	+	nuc	0	Nucleus (Probable)				223
Q86YM7 UniProt NPD GO	HOME1_HUMAN	Homer protein homolog 1	0.50	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells. Isoform 1 inhibits surface expres ...	integral to plasma membrane [TAS]	604798		354
Q86YZ3 UniProt NPD GO	HORN_HUMAN	Hornerin	0.50	-	nuc	0	Found in keratohyalin granules in the granular cells of the epidermis (By similarity)				2850
P53263 UniProt NPD GO	YG2U_YEAST	Hypothetical 17.4 kDa protein in VMA21-CLB1 intergenic region	0.50	-	mit	0					149
P38212 UniProt NPD GO	YBL5_YEAST	Hypothetical 23.9 kDa protein in COQ1-UGA5 intergenic region	0.50	-	nuc	1 *		integral to endoplasmic reticulum membrane [IDA]			213
P36125 UniProt NPD GO	YK10_YEAST	Hypothetical 32.0 kDa protein in SAP190-SPO14 intergenic region	0.50	-	end	5		integral to Golgi membrane [IDA]			273
P46983 UniProt NPD GO	YJS5_YEAST	Hypothetical 33.7 kDa protein in SWE1-ATP12 intergenic region	0.50	-	nuc	0					293
Q04471 UniProt NPD GO	YM04_YEAST	Hypothetical 42.9 kDa protein in ILV2-ADE17 intergenic region	0.50	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			368
P48236 UniProt NPD GO	YG3L_YEAST	Hypothetical 51.6 kDa protein in RPL24B-RSR1 intergenic region	0.50	-	cyt	7	Membrane; multi-pass membrane protein (Potential)				432
P38721 UniProt NPD GO	YHF0_YEAST	Hypothetical 79.0 kDa protein in CBP2 5'region	0.50	+	nuc	0	Membrane; multi-pass membrane protein (Potential)				697
Q9P7I3 UniProt NPD GO	YIRF_SCHPO	Hypothetical WD repeat protein C664.15 in chromosome I	0.50	-	nuc	0					651
Q11178 UniProt NPD GO	YPC1_CAEEL	Hypothetical protein C05D10.1	0.50	-	nuc	0					529
Q10203 UniProt NPD GO	YBX5_SCHPO	Hypothetical protein C17D1.05 in chromosome II	0.50	-	nuc	0					368
Q10111 UniProt NPD GO	YAQC_SCHPO	Hypothetical protein C18G6.12c in chromosome I	0.50	-	nuc	0					309
O14127 UniProt NPD GO	YF51_SCHPO	Hypothetical protein C3C7.01c in chromosome I	0.50	-	cyt	0					611
O14229 UniProt NPD GO	YDVB_SCHPO	Hypothetical protein C6F12.11c in chromosome I	0.50	-	nuc	0					456
Q8SV54 UniProt NPD GO	Y707_ENCCU	Hypothetical protein ECU07_0070	0.50	-	cyt	0					615
P34530 UniProt NPD GO	YM91_CAEEL	Hypothetical protein M01A8.1	0.50	-	nuc	0					203
Q9P7X3 UniProt NPD GO	YH6C_SCHPO	Hypothetical protein P23A10.12 in chromosome II	0.50	-	nuc	0					245
O08836 UniProt NPD GO	IGBP1_RAT	Immunoglobulin-binding protein 1 (CD79a-binding protein 1) (Alpha4 phosphoprotein)	0.50	-	nuc	0	Cytoplasm (Potential)				340
Q9QZ29 UniProt NPD GO	IGB1B_MOUSE	Immunoglobulin-binding protein 1b (CD79a-binding protein 1b) (Alpha 4-b protein) (Alpha4-b)	0.50	-	nuc	0	Cytoplasm (Potential)				343

You are viewing entries 25001 to 25050 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.