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
Q93XX8 UniProt NPD GO	NOLA3_ARATH	H/ACA ribonucleoprotein complex subunit 3-like protein	0.27	-	nuc	0	Nucleus; nucleolus (By similarity)				64
Q5R6Y0 UniProt NPD GO	HBS1L_PONPY	HBS1-like protein	0.27	-	mit	0					684
Q9Y450 UniProt NPD GO	HBS1L_HUMAN	HBS1-like protein (ERFS)	0.27	-	mit	0					684
P62691 UniProt NPD GO	GAK19_HUMAN	HERV-K_4p16.1 provirus ancestral Gag polyprotein (Gag polyprotein)	0.27	-	cyt	0					212
Q10370 UniProt NPD GO	HMGYB_SOYBN	HMG-Y-related protein B (SB16B protein) (Fragment)	0.27	-	nuc	0	Nucleus (Potential)				152
P26585 UniProt NPD GO	HMGL_SOYBN	HMG1/2-like protein (SB11 protein)	0.27	-	nuc	0	Nucleus (Potential)				152
P02827 UniProt NPD GO	HSP70_XENLA	Heat shock 70 kDa protein (HSP70)	0.27	-	cyt	0					647
P47773 UniProt NPD GO	HSP7C_ICTPU	Heat shock cognate 71 kDa protein	0.27	-	cyt	0					649
O97125 UniProt NPD GO	HSP68_DROME	Heat shock protein 68	0.27	-	cyt	0					635
Q18688 UniProt NPD GO	HSP90_CAEEL	Heat shock protein 90 (Abnormal dauer formation protein 21)	0.27	-	cyt	0	Cytoplasm; perinuclear region. Perinuclear region of somatic cells				702
Q5EAC9 UniProt NPD GO	HSPB8_BOVIN	Heat-shock protein beta-8 (HspB8)	0.27	-	nuc	0					196
P80960 UniProt NPD GO	HCY2A_RAPTH	Hemocyanin type 2 unit a (RtH2-a) (Hemocyanin Rta) (Hemocyanin RHSS2 subunit) (Hemocyanin heavy stru ...	0.27	-	cyt	0	Secreted protein; extracellular space				407
Q05187 UniProt NPD GO	TGMH_TACTR	Hemocyte protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13) (Hemocyte transglutaminase) (TGas ...	0.27	-	nuc	0	Membrane; peripheral membrane protein				764
P40625 UniProt NPD GO	HMG_TETPY	High mobility group protein (Nonhistone chromosomal protein)	0.27	-	nuc	0	Nucleus				99
P15516 UniProt NPD GO	HIS3_HUMAN	Histatin-3 precursor (Histidine-rich protein 3) (PB) (Basic histidine-rich protein) (Hst) [Contains: ...	0.27	-	mit	0	Secreted protein. Secreted by serous acinar and demilune cells	extracellular region [NAS]	142702		51
Q9LU15 UniProt NPD GO	AHP4_ARATH	Histidine-containing phosphotransfer protein 4	0.27	-	nuc	0					127
Q8L9T7 UniProt NPD GO	AHP5_ARATH	Histidine-containing phosphotransfer protein 5	0.27	-	nuc	0					157
Q8J0U2 UniProt NPD GO	H1_NEUCR	Histone H1	0.27	-	nuc	0	Nucleus (Potential)				236
P35060 UniProt NPD GO	H1_TIGCA	Histone H1	0.27	+	nuc	0	Nucleus				181
P08285 UniProt NPD GO	H103_CHICK	Histone H1.03	0.27	+	nuc	0	Nucleus				223
Q9SF55 UniProt NPD GO	H2B5_ARATH	Histone H2B.5 (HTB7)	0.27	-	nuc	0	Nucleus (By similarity)				125
P06353 UniProt NPD GO	H3_HORVU	Histone H3 (Fragment)	0.27	-	mit	0	Nucleus (By similarity)				80
P53920 UniProt NPD GO	YNM3_YEAST	Hypothetical 110.9 kDa protein in SPC98-TOM70 intergenic region	0.27	-	nuc	0		nucleus [IDA]			997
P33544 UniProt NPD GO	YM23_MAIZE	Hypothetical 33.9 kDa protein in mitochondrial linear 2.3 KB plasmid	0.27	-	nuc	0					294
Q04689 UniProt NPD GO	YMF0_YEAST	Hypothetical 36.0 kDa protein in GAL80-PRP39 intergenic region	0.27	-	mit	0					311
Q09357 UniProt NPD GO	YS02_CAEEL	Hypothetical UPF0049 protein ZK1128.2 in chromosome III	0.27	+	nuc	0					479
Q8MNU7 UniProt NPD GO	YLCG_CAEEL	Hypothetical UPF0287 protein C35D10.17 in chromosome III	0.27	-	nuc	0					102
P93284 UniProt NPD GO	M150_ARATH	Hypothetical mitochondrial protein AtMg00150 (ORF116)	0.27	-	nuc	1	Mitochondrion (Potential)				116
P92544 UniProt NPD GO	M1130_ARATH	Hypothetical mitochondrial protein AtMg01130 (ORF106f)	0.27	-	nuc	0	Mitochondrion (Potential)				106
P92567 UniProt NPD GO	M1410_ARATH	Hypothetical mitochondrial protein AtMg01410 (ORF204)	0.27	-	cyt	0	Mitochondrion (Potential)				204
P34259 UniProt NPD GO	YKA8_CAEEL	Hypothetical protein B0303.8	0.27	-	nuc	1					239
Q17528 UniProt NPD GO	YQE3_CAEEL	Hypothetical protein B0564.3 in chromosome IV	0.27	-	end	4 *					450
P34287 UniProt NPD GO	YKK0_CAEEL	Hypothetical protein C02F5.10	0.27	-	nuc	0					142
Q09445 UniProt NPD GO	YQ01_CAEEL	Hypothetical protein C04A2.1 in chromosome II	0.27	-	nuc	0					330
O94369 UniProt NPD GO	YG03_SCHPO	Hypothetical protein C1604.03c in chromosome II	0.27	-	mit	0					330
Q10160 UniProt NPD GO	YAU3_SCHPO	Hypothetical protein C26A3.03c in chromosome I	0.27	-	cyt	0		RecQ helicase-Topo III complex [IDA]			235
Q09810 UniProt NPD GO	YABA_SCHPO	Hypothetical protein C2G11.10c in chromosome I	0.27	-	nuc	0					401
Q09269 UniProt NPD GO	YQF4_CAEEL	Hypothetical protein C34C12.4	0.27	-	nuc	1 *					101
Q10260 UniProt NPD GO	YD2C_SCHPO	Hypothetical protein C56F8.12 in chromosome I	0.27	+	end	7	Membrane; multi-pass membrane protein (Potential)				394
Q92348 UniProt NPD GO	YDH3_SCHPO	Hypothetical protein C6G9.03c in chromosome I	0.27	-	mit	0					352
Q09277 UniProt NPD GO	YPX5_CAEEL	Hypothetical protein F40H6.5	0.27	-	exc	1 *	Membrane; multi-pass membrane protein (Potential)				1216
Q22566 UniProt NPD GO	YSV1_CAEEL	Hypothetical protein T19C3.1 in chromosome III	0.27	-	end	2					501
P34669 UniProt NPD GO	YO13_CAEEL	Hypothetical protein ZK686.3 in chromosome III	0.27	-	end	4	Membrane; multi-pass membrane protein (Potential)				331
Q32759 UniProt NPD GO	YCF70_ORYSA	Hypothetical protein ycf70 (ORF89)	0.27	-	mit	1 *	Plastid; chloroplast				89
O13854 UniProt NPD GO	YFGG_SCHPO	Hypothetical serine/threonine-rich protein C19G12.16c precursor	0.27	-	nuc	0	Secreted protein (Potential)	cell surface [TAS]			670
Q8BLR9 UniProt NPD GO	HIF1N_MOUSE	Hypoxia-inducible factor 1 alpha inhibitor (EC 1.14.11.16) (Hypoxia-inducible factor asparagine hydr ...	0.27	-	cyt	0	Nucleus (Potential)				349
Q8TC41 UniProt NPD GO	IBRD1_HUMAN	IBR domain-containing protein 1	0.27	-	mit	1		ubiquitin ligase complex [ISS]			275
P01618 UniProt NPD GO	KV1_CANFA	Ig kappa chain V region GOM	0.27	-	nuc	0					108
P04430 UniProt NPD GO	KV1V_HUMAN	Ig kappa chain V-I region BAN	0.27	-	nuc	0		extracellular region [NAS]			108
P01602 UniProt NPD GO	KV1J_HUMAN	Ig kappa chain V-I region HK102 precursor (Fragment)	0.27	-	exc	0		extracellular region [NAS]			117

You are viewing entries 43251 to 43300 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.