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
Q8X1E6 UniProt NPD GO	CDC37_CANAL	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (Cell division control p ...	0.46	-	nuc	0	Cytoplasm (By similarity)				508
P40211 UniProt NPD GO	YM21_YEAST	Hypothetical 12.1 kDa protein in MDS1-RPL13B intergenic region	0.46	-	nuc	2 *					102
Q03667 UniProt NPD GO	YMO2_YEAST	Hypothetical 16.7 kDa protein in CDC5-MVP1 intergenic region	0.46	-	mit	0		cytoplasm [IDA] nucleus [IDA]			156
P43540 UniProt NPD GO	YFG4_YEAST	Hypothetical 20.4 kDa protein in COS4 5'region	0.46	-	nuc	0					174
P48358 UniProt NPD GO	YCF21_CYAPA	Hypothetical 23.3 kDa protein ycf21	0.46	-	cyt	0	Plastid; cyanelle				193
P40206 UniProt NPD GO	YM16_YEAST	Hypothetical 24.7 kDa protein in POM152-REC114 intergenic region	0.46	-	nuc	0		cytoplasm [IDA]			208
O20133 UniProt NPD GO	YCX4_CHLVU	Hypothetical 27.2 kDa protein in rrn23-psbC intergenic region (ORF236)	0.46	-	nuc	0	Plastid; chloroplast				236
O20130 UniProt NPD GO	YCX3_CHLVU	Hypothetical 28.3 kDa protein in rrn23-psbC intergenic region (ORF250)	0.46	-	mit	0	Plastid; chloroplast				250
Q03691 UniProt NPD GO	YM56_YEAST	Hypothetical 28.9 kDa protein in CLN1-RAD14 intergenic region	0.46	-	nuc	1		endoplasmic reticulum [IDA]			256
P15613 UniProt NPD GO	YM12_PARTE	Hypothetical 31.1 kDa protein (ORF12)	0.46	-	nuc	0					265
P53722 UniProt NPD GO	YN8A_YEAST	Hypothetical 32.2 kDa protein in ARE2-SWP73 intergenic region	0.46	-	mit	0					270
P53156 UniProt NPD GO	YGI1_YEAST	Hypothetical 36.4 kDa protein in SCY1-DBP3 intergenic region	0.46	-	nuc	0					320
Q10437 UniProt NPD GO	YDE3_SCHPO	Hypothetical WD repeat protein C12B10.03 in chromosome I	0.46	+	cyt	0					543
P93295 UniProt NPD GO	M310_ARATH	Hypothetical mitochondrial protein AtMg00310 (ORF154)	0.46	-	cyt	0	Mitochondrion (Potential)				154
Q10921 UniProt NPD GO	YWQ1_CAEEL	Hypothetical protein B0286.1	0.46	-	nuc	0					230
O13743 UniProt NPD GO	YDR8_SCHPO	Hypothetical protein C16E8.08 in chromosome I	0.46	-	nuc	0					269
O13882 UniProt NPD GO	YE1I_SCHPO	Hypothetical protein C1B3.18c in chromosome I	0.46	-	nuc	1 *					223
Q10350 UniProt NPD GO	YDA8_SCHPO	Hypothetical protein C1F12.08 in chromosome I	0.46	-	cyt	0					329
Q10368 UniProt NPD GO	YDBI_SCHPO	Hypothetical protein C22E12.18 in chromosome I	0.46	+	cyt	0					336
P87150 UniProt NPD GO	YB09_SCHPO	Hypothetical protein C25H2.09 in chromosome II	0.46	-	nuc	0					162
O36024 UniProt NPD GO	YEKC_SCHPO	Hypothetical protein C4F10.12 in chromosome I	0.46	-	cyt	0		kinetochore [IDA]			280
Q8STB2 UniProt NPD GO	Y5G3_ENCCU	Hypothetical protein ECU05_1630/ECU11_0100	0.46	-	nuc	1 *					101
Q8SUU2 UniProt NPD GO	Y7I4_ENCCU	Hypothetical protein ECU07_1840	0.46	-	cyt	0					161
Q8SU96 UniProt NPD GO	YAI1_ENCCU	Hypothetical protein ECU10_1810	0.46	+	mit	0					621
Q09352 UniProt NPD GO	YRV9_CAEEL	Hypothetical protein T10B9.29 precursor	0.46	-	nuc	0					124
O89113 UniProt NPD GO	IER5_MOUSE	Immediate early response gene 5 protein	0.46	-	nuc	0					308
P13372 UniProt NPD GO	VPRE1_MOUSE	Immunoglobulin iota chain precursor (VPreB1 protein)	0.46	-	exc	0		plasma membrane [IPI]			142
P13373 UniProt NPD GO	VPRE2_MOUSE	Immunoglobulin omega chain precursor (VpreB2 protein)	0.46	-	exc	0					142
Q9JM04 UniProt NPD GO	IPO13_RAT	Importin-13 (Imp13) (Late gestation lung 2 protein)	0.46	-	ves	0	Cytoplasm (By similarity). Nucleus (By similarity)				963
Q00238 UniProt NPD GO	ICAM1_RAT	Intercellular adhesion molecule 1 precursor (ICAM-1)	0.46	-	end	2 *	Membrane; single-pass type I membrane protein	plasma membrane [IEP]			545
P81255 UniProt NPD GO	IFNA1_CANFA	Interferon alpha-1/2 precursor (IFN-alpha-1/2)	0.46	-	exc	0	Secreted protein				187
P01568 UniProt NPD GO	IFN21_HUMAN	Interferon alpha-21 precursor (Interferon alpha-F) (LeIF F)	0.46	-	mit	0	Secreted protein		147584		189
O97945 UniProt NPD GO	IFNA3_CANFA	Interferon alpha-3 precursor (IFN-alpha-3)	0.46	-	exc	0	Secreted protein				187
O18999 UniProt NPD GO	IL1RA_HORSE	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.46	-	exc	0	Secreted protein				177
O02814 UniProt NPD GO	IL12A_CAPHI	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.46	-	mit	0	Secreted protein				221
P48091 UniProt NPD GO	IL12A_MACMU	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.46	-	mit	0	Secreted protein				219
Q61729 UniProt NPD GO	IL12B_MARMO	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.46	-	exc	0	Secreted protein (By similarity)				327
O95256 UniProt NPD GO	I18RA_HUMAN	Interleukin-18 receptor accessory protein precursor (IL-18 receptor accessory protein) (IL-18RAcP) ( ...	0.46	-	end	1	Membrane; single-pass type I membrane protein (Potential)		604509		599
Q9ES17 UniProt NPD GO	IL21_MOUSE	Interleukin-21 precursor (IL-21)	0.46	-	nuc	0	Secreted protein				146
O35228 UniProt NPD GO	IL27B_MOUSE	Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein homolog)	0.46	-	exc	0	Secreted protein (By similarity)				228
P06740 UniProt NPD GO	IL3_HYLLA	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.46	-	exc	0	Secreted protein				152
P18520 UniProt NPD GO	ION3_CARAU	Intermediate filament protein ON3	0.46	-	nuc	0					520
Q96RY7 UniProt NPD GO	IF140_HUMAN	Intraflagellar transport 140 homolog (WD and tetratricopeptide repeats protein 2)	0.46	-	cyt	0					1462
Q6C423 UniProt NPD GO	JHD1_YARLI	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.46	-	cyt	0	Nucleus (By similarity)				510
Q9GKY8 UniProt NPD GO	JPH1_RABIT	Junctophilin-1 (Junctophilin type 1) (JP-1) (Mitsugumin-72) (Mg72)	0.46	-	nuc	1	Cell membrane; peripheral membrane protein (By similarity). Endoplasmic reticulum; endoplasmic retic ...				662
Q5XIK7 UniProt NPD GO	KATL1_RAT	Katanin p60 ATPase-containing subunit A-like 1 (EC 3.6.4.3) (Katanin p60 subunit A-like 1) (p60 kata ...	0.46	-	nuc	0					488
O76009 UniProt NPD GO	K1HA_HUMAN	Keratin, type I cuticular Ha3-I (Hair keratin, type I Ha3-I)	0.46	-	nuc	0			602761		404
Q8JFQ6 UniProt NPD GO	K1C13_ONCMY	Keratin, type I cytoskeletal 13 (Cytokeratin-13) (CK-13) (Keratin-13) (K13)	0.46	-	nuc	0					492
Q9BYU7 UniProt NPD GO	KR413_HUMAN	Keratin-associated protein 4-13 (Keratin-associated protein 4.13) (Ultrahigh sulfur keratin-associat ...	0.46	-	nuc	0					106
Q9BYQ6 UniProt NPD GO	KR414_HUMAN	Keratin-associated protein 4-14 (Keratin-associated protein 4.14) (Ultrahigh sulfur keratin-associat ...	0.46	-	nuc	0					195

You are viewing entries 27701 to 27750 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.