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
P22431 UniProt NPD GO	GLB3_CHITP	Globin CTP-III (Erythrocruorin III)	0.00	-	cyt	0					136
P11582 UniProt NPD GO	GLBE_CHITH	Globin CTT-E/E' precursor	0.00	-	exc	0					152
P02221 UniProt NPD GO	GLB1_CHITH	Globin CTT-I/CTT-IA precursor (Erythrocruorin)	0.00	-	exc	0					158
P02222 UniProt NPD GO	GLB2_CHITH	Globin CTT-II beta precursor	0.00	-	exc	0					160
P02229 UniProt NPD GO	GLB3_CHITH	Globin CTT-III precursor (Erythrocruorin III)	0.00	-	exc	0				1ECO	151
P02231 UniProt NPD GO	GLBT_CHITH	Globin CTT-IIIA	0.00	-	cyt	0					151
P02230 UniProt NPD GO	GLB4_CHITH	Globin CTT-IV precursor	0.00	-	end	0					151
P02223 UniProt NPD GO	GLB9_CHITH	Globin CTT-IX precursor	0.00	-	end	0					161
P29243 UniProt NPD GO	GLBV_CHITP	Globin CTT-V precursor (HBV)	0.00	-	vac	0					163
P02226 UniProt NPD GO	GLB7A_CHITH	Globin CTT-VIIA precursor	0.00	-	end	0					161
Q23762 UniProt NPD GO	GLB7X_CHITH	Globin CTT-VIIB-10 precursor	0.00	-	vac	0					161
P12548 UniProt NPD GO	GLB73_CHITH	Globin CTT-VIIB-3 precursor	0.00	-	vac	0					161
P84297 UniProt NPD GO	GLB74_CHITP	Globin CTT-VIIB-4 precursor	0.00	-	end	0					161
P84296 UniProt NPD GO	GLB74_CHITH	Globin CTT-VIIB-4 precursor (Erythrocruorin)	0.00	-	end	0					161
P84298 UniProt NPD GO	GLB75_CHITH	Globin CTT-VIIB-5/CTT-VIIB-9 precursor	0.00	-	vac	0					161
P84299 UniProt NPD GO	GLB75_CHITP	Globin CTT-VIIB-5/CTT-VIIB-9 precursor	0.00	-	vac	0					161
P12549 UniProt NPD GO	GLB76_CHITH	Globin CTT-VIIB-6 precursor	0.00	-	vac	0					161
P12550 UniProt NPD GO	GLB77_CHITH	Globin CTT-VIIB-7 precursor	0.00	-	exc	0					162
P29242 UniProt NPD GO	GLB77_CHITP	Globin CTT-VIIB-7 precursor	0.00	-	exc	0					162
Q23763 UniProt NPD GO	GLB78_CHITH	Globin CTT-VIIB-8 precursor	0.00	-	vac	0					161
P18966 UniProt NPD GO	GLB78_CHITP	Globin CTT-VIIB-8 precursor	0.00	-	vac	0					161
P02227 UniProt NPD GO	GLB8_CHITH	Globin CTT-VIII	0.00	-	cyt	0					151
Q23760 UniProt NPD GO	GLBW_CHITH	Globin CTT-W precursor (HBW)	0.00	-	end	0					159
P29244 UniProt NPD GO	GLBW_CHITP	Globin CTT-W precursor (HBW)	0.00	-	end	0					159
P02228 UniProt NPD GO	GLB10_CHITH	Globin CTT-X	0.00	-	cyt	0					151
P18968 UniProt NPD GO	GLBY_CHITP	Globin CTT-Y precursor (HBY)	0.00	-	vac	0					160
Q23761 UniProt NPD GO	GLBZ_CHITH	Globin CTT-Z precursor (HBZ)	0.00	-	vac	0					163
P29245 UniProt NPD GO	GLBZ_CHITP	Globin CTT-Z precursor (HBZ)	0.00	-	vac	0					163
P02216 UniProt NPD GO	GLB1_GLYDI	Globin, major monomeric component	0.00	-	mit	0				2HBG	147
P25165 UniProt NPD GO	GLBM_ANATR	Globin, minor	0.00	-	cyt	0					151
P15447 UniProt NPD GO	GLB4_GLYDI	Globin, monomeric component M-IV (GMH4)	0.00	-	mit	0				1VRF	147
P21659 UniProt NPD GO	GLBP2_GLYDI	Globin, polymeric component P2	0.00	-	cyt	0					147
P21660 UniProt NPD GO	GLBP3_GLYDI	Globin, polymeric component P3	0.00	-	mit	0					147
P14805 UniProt NPD GO	GLB1_CALSO	Globin-1 (Globin I) (Hb I)	0.00	-	cyt	1					144
P02212 UniProt NPD GO	GLB1_ANABR	Globin-1 (Globin I) (HbI)	0.00	-	cyt	0	Cytoplasm				146
P02213 UniProt NPD GO	GLB1_SCAIN	Globin-1 (Globin I) (HbI) (Dimeric hemoglobin)	0.00	-	cyt	0	Cytoplasm			7HBI	146
P21197 UniProt NPD GO	GLB1_MORMR	Globin-1 (Hemoglobin I)	0.00	-	cyt	0					149
P14395 UniProt NPD GO	GLB1A_ANATR	Globin-1 subunit alpha (Globin I alpha chain)	0.00	-	cyt	0					150
P04251 UniProt NPD GO	GLB1B_ANATR	Globin-1 subunit beta (Globin I beta chain)	0.00	-	mit	0					151
Q9I9I3 UniProt NPD GO	GLB2_PETMA	Globin-2 (Globin II) (Hemoglobin PmII')	0.00	-	cyt	0					149
P21198 UniProt NPD GO	GLB2_MORMR	Globin-2 (Hemoglobin II)	0.00	-	cyt	0					149
P14821 UniProt NPD GO	GLB2A_SCAIN	Globin-2 A chain (Globin II A chain) (HBII-A)	0.00	-	cyt	0				1SCT	149
P14822 UniProt NPD GO	GLB2B_SCAIN	Globin-2 B chain (Globin II B chain) (HBII-B)	0.00	-	cyt	0				1SCT	151
P09968 UniProt NPD GO	GLB3_PETMA	Globin-3 (Globin III)	0.00	-	cyt	0					149
P21199 UniProt NPD GO	GLB3_MORMR	Globin-3 (Hemoglobin III)	0.00	-	cyt	0					149
P02208 UniProt NPD GO	GLB5_PETMA	Globin-5 (Hemoglobin V)	0.00	-	cyt	0				3LHB	149
Q7Z9L3 UniProt NPD GO	EXG_ASPOR	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.00	-	exc	0	Secreted protein				405
O13738 UniProt NPD GO	GNA1_SCHPO	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.00	-	mit	0					111
Q64422 UniProt NPD GO	GNPI_MESAU	Glucosamine-6-phosphate isomerase (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase) (GNPDA) (GlcN6P ...	0.00	-	cyt	0	Cytoplasm (By similarity)				289
O88958 UniProt NPD GO	GNPI_MOUSE	Glucosamine-6-phosphate isomerase (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase) (GNPDA) (GlcN6P ...	0.00	-	cyt	0	Cytoplasm				289

You are viewing entries 94701 to 94750 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.