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
Q9UQL6 UniProt NPD GO	HDAC5_HUMAN	Histone deacetylase 5 (HD5) (Antigen NY-CO-9)	0.82	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm. In muscle cells, it shuttles int ...	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]	605315		1122
Q9Z2V6 UniProt NPD GO	HDAC5_MOUSE	Histone deacetylase 5 (HD5) (Histone deacetylase mHDA1)	0.82	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm. ...	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			1113
Q9UKV0 UniProt NPD GO	HDAC9_HUMAN	Histone deacetylase 9 (HD9) (HD7B) (HD7)	0.82	-	nuc	0	Nucleus (By similarity)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [NAS]	606543		1011
P32480 UniProt NPD GO	HIR2_YEAST	Histone transcription regulator 2	0.82	-	nuc	0	Nucleus	nucleus [IDA]			875
Q90655 UniProt NPD GO	AKR_CHICK	Homeobox protein AKR (Avian knotted-related protein)	0.82	-	nuc	0	Nucleus				269
Q91907 UniProt NPD GO	GBX2_XENLA	Homeobox protein GBX-2 (Gastrulation and brain-specific homeobox protein 2) (XGBX-2)	0.82	+	nuc	0	Nucleus (Probable)				340
Q91771 UniProt NPD GO	HXB7A_XENLA	Homeobox protein Hox-B7 A (XlHbox-2 A) (MM3)	0.82	+	nuc	0	Nucleus				220
P09632 UniProt NPD GO	HXB8_MOUSE	Homeobox protein Hox-B8 (Hox-2.4)	0.82	+	nuc	0	Nucleus				243
P17481 UniProt NPD GO	HXB8_HUMAN	Homeobox protein Hox-B8 (Hox-2D) (Hox-2.4)	0.82	+	nuc	0	Nucleus	nucleus [NAS]	142963		243
P09017 UniProt NPD GO	HXC4_HUMAN	Homeobox protein Hox-C4 (Hox-3E) (CP19)	0.82	+	nuc	0	Nucleus	nucleus [NAS]	142974		264
Q9YH13 UniProt NPD GO	HXC8_CHICK	Homeobox protein Hox-C8 (cHoxc-8)	0.82	+	nuc	0	Nucleus (By similarity)				242
Q9IA15 UniProt NPD GO	HXD11_HETFR	Homeobox protein Hox-D11	0.82	+	nuc	0	Nucleus (By similarity)				265
O57374 UniProt NPD GO	HXD4A_BRARE	Homeobox protein Hox-D4a (Hox-D4)	0.82	+	nuc	0	Nucleus				236
P23459 UniProt NPD GO	HXD8_CHICK	Homeobox protein Hox-D8 (Chox-M)	0.82	+	nuc	0	Nucleus				188
Q9IA13 UniProt NPD GO	HXD9_HETFR	Homeobox protein Hox-D9	0.82	+	nuc	0	Nucleus (By similarity)				265
P39021 UniProt NPD GO	MEOX2_XENLA	Homeobox protein MOX-2	0.82	+	nuc	0	Nucleus (Potential)				298
P29454 UniProt NPD GO	GSCA_XENLA	Homeobox protein goosecoid isoform A	0.82	+	nuc	0	Nucleus				243
P34684 UniProt NPD GO	LIN39_CAEEL	Homeobox protein lin-39 (Abnormal cell lineage protein 39)	0.82	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			253
P10038 UniProt NPD GO	MAB5_CAEEL	Homeobox protein mab-5 (Protein male abnormal 5)	0.82	+	nuc	0	Nucleus (Probable)				200
P32314 UniProt NPD GO	FOXN2_HUMAN	Human T-cell leukemia virus enhancer factor (Forkhead box protein N2)	0.82	-	nuc	0	Nucleus		143089		341
P40449 UniProt NPD GO	YIQ1_YEAST	Hypothetical 27.1 kDa protein in SUC2-FOX3 intergenic region	0.82	-	nuc	0		cytoplasm [IDA]			235
P39983 UniProt NPD GO	YEG7_YEAST	Hypothetical 27.2 kDa protein in PCM1-HAT2 intergenic region	0.82	-	nuc	0					233
P53907 UniProt NPD GO	YNO4_YEAST	Hypothetical 84.2 kDa protein in MFA2-MEP2 intergenic region	0.82	-	nuc	0		mitochondrion [IDA]			740
P92525 UniProt NPD GO	M870_ARATH	Hypothetical mitochondrial protein AtMg00870 (ORF184)	0.82	-	nuc	0	Mitochondrion (Potential)				184
Q9C8Z4 UniProt NPD GO	HEAT1_ARATH	Hypothetical protein At3g06530	0.82	-	mit	0	Nucleus; nucleolus (By similarity)				1830
O13719 UniProt NPD GO	YDZC_SCHPO	Hypothetical protein C14C4.12c in chromosome I	0.82	-	nuc	0					297
Q9P7H8 UniProt NPD GO	YLK1_SCHPO	Hypothetical protein C1782.01 in chromosome I	0.82	-	cyt	0					1679
Q9P7Q6 UniProt NPD GO	YFV9_SCHPO	Hypothetical protein C1834.09 in chromosome I	0.82	+	nuc	0					306
Q10030 UniProt NPD GO	YQ91_CAEEL	Hypothetical protein C27D6.1	0.82	-	nuc	0					782
Q9USV4 UniProt NPD GO	YHH2_SCHPO	Hypothetical protein C28F2.02 in chromosome II	0.82	-	nuc	0		cytoplasm [IDA]			292
Q09706 UniProt NPD GO	YA2G_SCHPO	Hypothetical protein C2F7.16c in chromosome I	0.82	-	nuc	0					1369
O14360 UniProt NPD GO	YB4F_SCHPO	Hypothetical protein C30D10.15 in chromosome II	0.82	+	nuc	0					516
P87318 UniProt NPD GO	YB2H_SCHPO	Hypothetical protein C31F10.17c in chromosome II	0.82	-	nuc	0					135
O14180 UniProt NPD GO	YDS4_SCHPO	Hypothetical protein C4F8.04 in chromosome I	0.82	+	nuc	0					306
Q8ST93 UniProt NPD GO	Y703_ENCCU	Hypothetical protein ECU07_0030/ECU09_2040	0.82	-	nuc	0					236
P34524 UniProt NPD GO	YM63_CAEEL	Hypothetical protein K12H4.3 in chromosome III	0.82	+	nuc	0					352
Q09345 UniProt NPD GO	YRR2_CAEEL	Hypothetical protein R144.2	0.82	-	nuc	0					823
Q22836 UniProt NPD GO	YGH1_CAEEL	Hypothetical protein T27F2.1 in chromosome V	0.82	-	nuc	0					535
Q8VEK6 UniProt NPD GO	ING3_MOUSE	Inhibitor of growth protein 3 (p47ING3 protein)	0.82	-	nuc	0	Nucleus (By similarity)				421
P30123 UniProt NPD GO	IFNG_RABIT	Interferon gamma precursor (IFN-gamma)	0.82	+	exc	0	Secreted protein			2RIG	167
Q9TV67 UniProt NPD GO	IFNG_TURTR	Interferon gamma precursor (IFN-gamma)	0.82	+	exc	0	Secreted protein (By similarity)				166
Q55NZ6 UniProt NPD GO	JHD1_CRYNE	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.82	-	nuc	0	Nucleus (By similarity)				879
Q6IRB8 UniProt NPD GO	JD2AA_XENLA	JmjC domain-containing histone demethylation protein 2A-A (EC 1.14.11.-) (Jumonji domain-containing ...	0.82	-	nuc	0	Nucleus (By similarity)				1331
P17210 UniProt NPD GO	KINH_DROME	Kinesin heavy chain	0.82	-	nuc	0		kinesin complex [IDA]			975
Q92376 UniProt NPD GO	KLP1_SCHPO	Kinesin-like protein 1	0.82	-	nuc	0	Nucleus	nucleus [IDA]			832
O14343 UniProt NPD GO	KLP5_SCHPO	Kinesin-like protein 5	0.82	-	mit	0	Cytoplasm. Cytoplasmic microtubules in interphase, mitotic kinetochores in metaphase and spindle mid ...	kinetochore [IDA] microtubule cytoskeleton [IDA] spindle midzone [IDA]			883
Q6FXI5 UniProt NPD GO	CIN8_CANGA	Kinesin-like protein CIN8	0.82	-	nuc	0	Spindle (By similarity). Spindle microtubules that lie between the poles (By similarity)				988
Q960Z0 UniProt NPD GO	KI10A_DROME	Kinesin-like protein Klp10A (Kinesin-like protein at cytological position 10A)	0.82	-	nuc	0	Centrosome. Localizes to mitotic centrosomes, spindle poles and centromeres through metaphase. Howev ...	kinetochore microtubule [IDA]			805
P08155 UniProt NPD GO	KRUH_DROME	Krueppel homologous protein 1	0.82	-	nuc	0					845
Q16787 UniProt NPD GO	LAMA3_HUMAN	Laminin alpha-3 chain precursor (Epiligrin 170 kDa subunit) (E170) (Nicein subunit alpha)	0.82	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [TAS]	600805		1713

You are viewing entries 7851 to 7900 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.