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
P51593 UniProt NPD GO	HUWE1_RAT	HECT, UBA and WWE domain-containing protein 1 (EC 6.3.2.-) (E3 ubiquitin protein ligase URE-B1) (Ups ...	0.26	-	cyt	0	Nucleus	nucleus [IDA]			322
P05456 UniProt NPD GO	HSP70_TRYCR	Heat shock 70 kDa protein	0.26	-	cyt	0					680
Q61316 UniProt NPD GO	HSP74_MOUSE	Heat shock 70 kDa protein 4 (Heat shock 70-related protein APG-2)	0.26	-	nuc	0	Cytoplasm (Probable)				841
P11141 UniProt NPD GO	HSP7F_CAEEL	Heat shock 70 kDa protein F, mitochondrial precursor	0.26	-	mit	0	Mitochondrion				657
P36415 UniProt NPD GO	HSP7C_DICDI	Heat shock cognate protein (Aginactin)	0.26	-	cyt	0	Cytoplasm. Found in F-actin-rich regions of the cell cortex and cell protrusions				640
P05812 UniProt NPD GO	HSP6A_DROME	Heat shock protein 67B1	0.26	-	cyt	0					238
Q01877 UniProt NPD GO	HSP71_PUCGR	Heat shock protein HSS1	0.26	-	cyt	0	Cytoplasm (Potential)				648
O74225 UniProt NPD GO	HSP88_NEUCR	Heat shock protein Hsp88	0.26	-	cyt	0	Cytoplasm				707
O73688 UniProt NPD GO	HMOX_FUGRU	Heme oxygenase (EC 1.14.99.3) (HO)	0.26	-	nuc	1	Microsome (By similarity)				277
P22796 UniProt NPD GO	HRL2_LACMU	Hemorrhagic factor II (EC 3.4.24.-) (LHF-II)	0.26	-	nuc	0					200
Q8JIR2 UniProt NPD GO	HR1A_TRIFL	Hemorrhagic metalloproteinase HR1a precursor (EC 3.4.24.-) [Contains: Disintegrin-like 1a]	0.26	+	nuc	0	Secreted protein				609
Q13151 UniProt NPD GO	ROA0_HUMAN	Heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)	0.26	+	cyt	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS]			305
P40632 UniProt NPD GO	NHP1_BABBO	High mobility group protein homolog NHP1	0.26	+	nuc	0	Nucleus (Potential)				97
P15515 UniProt NPD GO	HIS1_HUMAN	Histatin-1 precursor (Histidine-rich protein 1) (Post-PB protein) (PPB) [Contains: Histatin-2]	0.26	-	vac	0		extracellular region [NAS]	142701		57
P09987 UniProt NPD GO	H1_CHICK	Histone H1	0.26	+	nuc	0	Nucleus				217
P19375 UniProt NPD GO	H1E_STRPU	Histone H1, early embryonic	0.26	+	nuc	0	Nucleus				205
P08287 UniProt NPD GO	H11L_CHICK	Histone H1.11L	0.26	+	nuc	0	Nucleus			1GHC	224
P08288 UniProt NPD GO	H11R_CHICK	Histone H1.11R	0.26	+	nuc	0	Nucleus				218
Q6C4I6 UniProt NPD GO	H2A_YARLI	Histone H2A	0.26	-	nuc	0	Nucleus (By similarity)				134
Q4PEF8 UniProt NPD GO	H2B_USTMA	Histone H2B	0.26	-	nuc	0	Nucleus (By similarity)				141
P91849 UniProt NPD GO	H4_APIME	Histone H4	0.26	-	cyt	0	Nucleus (By similarity)				102
Q27443 UniProt NPD GO	H4_ASCSU	Histone H4	0.26	-	cyt	0	Nucleus (By similarity)				102
Q8LJS2 UniProt NPD GO	HD2A_SOYBN	Histone deacetylase 2a (HD2a) (Nucleolar histone deacetylase HD2-p39)	0.26	-	nuc	0	Nucleus; nucleolus (By similarity)				295
Q8SR09 UniProt NPD GO	HD2_ENCCU	Homeobox protein HD-2 (EcHD-2)	0.26	-	cyt	0	Nucleus (Potential)				192
Q9HGK2 UniProt NPD GO	MEU13_SCHPO	Homologous pairing protein meu13 (Meiotic expression up-regulated protein 13)	0.26	-	nuc	0	Nucleus				216
P36055 UniProt NPD GO	YKP8_YEAST	Hypothetical 11.4 kDa protein in PIR3-APE2 intergenic region	0.26	-	mit	0					100
P53216 UniProt NPD GO	YG1H_YEAST	Hypothetical 11.7 kDa protein in VMA7-RPS25A intergenic region	0.26	-	nuc	0					100
P36064 UniProt NPD GO	YKN7_YEAST	Hypothetical 12.0 kDa protein in MRPL31-APL2 intergenic region	0.26	-	mit	0					103
P34780 UniProt NPD GO	YCX6_ASTLO	Hypothetical 13.3 kDa protein in rpl23-rpl2 intergenic region (ORF105)	0.26	+	end	2 *	Plastid				105
P47151 UniProt NPD GO	YJ84_YEAST	Hypothetical 14.0 kDa protein in NNF1-STE24 intergenic region	0.26	-	nuc	0					130
P51216 UniProt NPD GO	YCX6_PORPU	Hypothetical 14.2 kDa protein in apcF-rps4 intergenic region (ORF121)	0.26	-	nuc	0	Plastid; chloroplast				121
P25629 UniProt NPD GO	YCT9_YEAST	Hypothetical 16.0 kDa protein in ARE1-THR4 intergenic region	0.26	-	nuc	0					148
P53269 UniProt NPD GO	YG31_YEAST	Hypothetical 27.2 kDa protein in SHY1-SPT6 intergenic region	0.26	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				259
P48338 UniProt NPD GO	YCX6_EUGGR	Hypothetical 32.3 kDa protein in rbcL-atpE intergenic region (ORF274)	0.26	-	mit	0	Plastid; chloroplast				274
P53217 UniProt NPD GO	YG1I_YEAST	Hypothetical 33.3 kDa protein in VMA7-RPS25A intergenic region	0.26	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				278
P49534 UniProt NPD GO	YCF39_ODOSI	Hypothetical 36.3 kDa protein ycf39 (ORF319)	0.26	-	mit	0	Plastid; chloroplast				319
P36081 UniProt NPD GO	YKH7_YEAST	Hypothetical 46.0 kDa protein in SMY1-MUD2 intergenic region	0.26	+	end	1		vacuole (sensu Fungi) [IDA]			392
Q11083 UniProt NPD GO	YT67_CAEEL	Hypothetical calcium-binding protein B0563.7 in chromosome X	0.26	-	nuc	0					229
P05475 UniProt NPD GO	YKP9_KLULA	Hypothetical killer plasmid pGKl-2 protein 9	0.26	-	cyt	0					453
Q11099 UniProt NPD GO	YL13_CAEEL	Hypothetical protein C02F12.3 precursor	0.26	-	mit	0					101
Q9USM2 UniProt NPD GO	YCLF_SCHPO	Hypothetical protein C16A11.15c in chromosome III	0.26	-	mit	0					117
Q10151 UniProt NPD GO	YAT5_SCHPO	Hypothetical protein C1D4.05c in chromosome I	0.26	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				387
Q10299 UniProt NPD GO	YD45_SCHPO	Hypothetical protein C22H10.05c in chromosome I	0.26	-	cyt	0					456
Q09680 UniProt NPD GO	YA0C_SCHPO	Hypothetical protein C5H10.12c in chromosome I	0.26	-	mit	1 *					371
Q8SW17 UniProt NPD GO	Y3C0_ENCCU	Hypothetical protein ECU03_1200	0.26	-	cyt	0					139
Q19683 UniProt NPD GO	YZR5_CAEEL	Hypothetical protein F21D5.5	0.26	-	nuc	0					407
Q09421 UniProt NPD GO	YRN7_CAEEL	Hypothetical protein R07B1.7	0.26	-	nuc	0					238
P82632 UniProt NPD GO	SCR13_ARATH	Hypothetical protein SCRL13 precursor	0.26	-	nuc	1 *					95
P34566 UniProt NPD GO	YNV3_CAEEL	Hypothetical protein T16H12.3	0.26	-	nuc	0					297
P34636 UniProt NPD GO	YOO4_CAEEL	Hypothetical protein ZK507.4	0.26	-	exc	0					206

You are viewing entries 44251 to 44300 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.