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
P50566 UniProt NPD GO	H4_CHLRE	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102
Q9HDF5 UniProt NPD GO	H4_MORAP	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102
P04914 UniProt NPD GO	H4_NEUCR	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102
P62792 UniProt NPD GO	H4_PHACH	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102
P04915 UniProt NPD GO	H4_PHYPO	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102
Q711M0 UniProt NPD GO	H41_PENFN	Histone H4.1	0.34	-	cyt	0	Nucleus (By similarity)				102
O14627 UniProt NPD GO	CDX4_HUMAN	Homeobox protein CDX-4 (Caudal-type homeobox protein 4)	0.34	+	nuc	0	Nucleus (By similarity)		300025		284
Q06736 UniProt NPD GO	MET2_SACPS	Homoserine O-acetyltransferase (EC 2.3.1.31) (Homoserine O-trans-acetylase)	0.34	-	nuc	0					486
Q04893 UniProt NPD GO	YM96_YEAST	Hypothetical 113.1 kDa protein in PRE5-FET4 intergenic region	0.34	-	mit	0					1140
P53888 UniProt NPD GO	YNR0_YEAST	Hypothetical 14.7 kDa protein in RPS3-PSD1 intergenic region	0.34	-	nuc	0					131
O88784 UniProt NPD GO	YIF3_MOUSE	Hypothetical 17.2 kDa IF3-like protein	0.34	-	nuc	0					147
P50945 UniProt NPD GO	YNK0_YEAST	Hypothetical 27.0 kDa protein in POL1-RAS2 intergenic region	0.34	-	nuc	0		mitochondrion [IDA]			234
P46996 UniProt NPD GO	YJQ3_YEAST	Hypothetical 61.5 kDa protein in TPK1-CCW7 intergenic region	0.34	-	end	12	Membrane; multi-pass membrane protein (Potential)				555
P25370 UniProt NPD GO	YCD6_YEAST	Hypothetical 64.9 kDa protein in SRO9-STE50 intergenic region	0.34	-	nuc	0					566
Q9FGD6 UniProt NPD GO	DOF58_ARATH	Hypothetical Dof zinc finger protein DOF5.8 (AtDOF5.8)	0.34	-	nuc	0	Nucleus (Probable)				225
P34293 UniProt NPD GO	YKO5_CAEEL	Hypothetical F-box protein C05B5.5	0.34	-	cyt	0					292
P92556 UniProt NPD GO	M1260_ARATH	Hypothetical mitochondrial protein AtMg01260 (ORF205)	0.34	-	mit	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				205
Q11075 UniProt NPD GO	YWV1_CAEEL	Hypothetical protein B0403.1	0.34	-	nuc	0					198
O14364 UniProt NPD GO	YOHB_SCHPO	Hypothetical protein C13E7.11 in chromosome II	0.34	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				298
Q9UTI1 UniProt NPD GO	YKZA_SCHPO	Hypothetical protein C15E1.10 in chromosome I	0.34	-	nuc	0					265
O94729 UniProt NPD GO	YG0H_SCHPO	Hypothetical protein C1604.17c in chromosome II	0.34	-	nuc	0					459
Q10062 UniProt NPD GO	YAM7_SCHPO	Hypothetical protein C1F5.07c in chromosome I	0.34	-	nuc	0					490
O13942 UniProt NPD GO	YEPC_SCHPO	Hypothetical protein C23H3.12c in chromosome I	0.34	-	mit	1					226
Q09248 UniProt NPD GO	YP9C_CAEEL	Hypothetical protein C28H8.12	0.34	-	nuc	0					331
P34350 UniProt NPD GO	YK84_CAEEL	Hypothetical protein C30A5.4	0.34	-	nuc	0					378
P46580 UniProt NPD GO	YLB5_CAEEL	Hypothetical protein C34E10.5	0.34	-	cyt	0					734
P48322 UniProt NPD GO	YPJ1_CAEEL	Hypothetical protein C36E8.1 in chromosome III	0.34	-	cyt	0					654
P53404 UniProt NPD GO	Y46K_DROME	Hypothetical protein CG10349 in chromosome 3	0.34	-	nuc	0					417
Q19005 UniProt NPD GO	YYT6_CAEEL	Hypothetical protein D2096.6	0.34	-	mit	0					171
Q8SU90 UniProt NPD GO	YB03_ENCCU	Hypothetical protein ECU11_0030	0.34	-	cyt	0					641
P34384 UniProt NPD GO	YLPD_CAEEL	Hypothetical protein F02A9.4b	0.34	-	mit	0					394
P34392 UniProt NPD GO	YLS7_CAEEL	Hypothetical protein F09G8.7	0.34	-	nuc	0					100
Q9HDX6 UniProt NPD GO	YK1E_SCHPO	Hypothetical protein PB1A10.14 in chromosome I	0.34	-	mit	0					243
P34645 UniProt NPD GO	YOQ7_CAEEL	Hypothetical protein ZK512.7	0.34	-	vac	0					141
Q09619 UniProt NPD GO	YS76_CAEEL	Hypothetical protein ZK892.6	0.34	-	cyt	0					237
O13695 UniProt NPD GO	YEN1_SCHPO	Hypothetical serine-rich protein C11G7.01 in chromosome I	0.34	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				536
O21266 UniProt NPD GO	YMF16_RECAM	Hypothetical tatC-like protein ymf16	0.34	-	end	7 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				260
P01610 UniProt NPD GO	KV1R_HUMAN	Ig kappa chain V-I region WEA	0.34	-	nuc	0		extracellular region [NAS]			108
P18135 UniProt NPD GO	KV3L_HUMAN	Ig kappa chain V-III region HAH precursor	0.34	-	nuc	0		extracellular region [NAS]			129
P01620 UniProt NPD GO	KV3B_HUMAN	Ig kappa chain V-III region SIE	0.34	-	nuc	0		extracellular region [NAS]			109
P04946 UniProt NPD GO	KV5U_MOUSE	Ig kappa chain V-V region NQ5-89.4	0.34	-	nuc	0					108
P04942 UniProt NPD GO	KV6H_MOUSE	Ig kappa chain V-VI region NQ5-61.1.2	0.34	-	nuc	0					107
P04944 UniProt NPD GO	KV6J_MOUSE	Ig kappa chain V-VI region NQ5-78.2.6	0.34	-	mit	0					107
P04943 UniProt NPD GO	KV6I_MOUSE	Ig kappa chain V-VI region NQ6-8.3.1	0.34	-	nuc	0					107
Q6CW96 UniProt NPD GO	TIM21_KLULA	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.34	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				234
P52292 UniProt NPD GO	IMA2_HUMAN	Importin alpha-2 subunit (Karyopherin alpha-2 subunit) (SRP1-alpha) (RAG cohort protein 1)	0.34	-	mit	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleoplasm [TAS] nucleus [TAS]	600685	1QGR	529
O35344 UniProt NPD GO	IMA3_MOUSE	Importin alpha-3 subunit (Karyopherin alpha-3 subunit) (Importin alpha Q2)	0.34	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				521
P55101 UniProt NPD GO	INHA_HORSE	Inhibin alpha chain precursor	0.34	-	exc	0	Secreted protein	extracellular region [ISS]			367
P55104 UniProt NPD GO	INHBC_MOUSE	Inhibin beta C chain precursor (Activin beta-C chain)	0.34	-	vac	0	Secreted protein (By similarity)				352
Q9WUK5 UniProt NPD GO	INHBC_RAT	Inhibin beta C chain precursor (Activin beta-C chain)	0.34	-	vac	0	Secreted protein (By similarity)				351

You are viewing entries 36751 to 36800 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.