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
Q22285 UniProt NPD GO	YFMO_CAEEL	Transthyretin-like protein T07C12.7 precursor	0.13	-	exc	0	Secreted protein (Potential)				179
Q8NIH6 UniProt NPD GO	TRI5_FUSAS	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.13	-	cyt	0					375
Q8NIC1 UniProt NPD GO	TRI5_FUSCE	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.13	-	cyt	0					375
Q7LJF8 UniProt NPD GO	TRI5_FUSCO	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.13	-	cyt	0					375
Q8NIC8 UniProt NPD GO	TRI5_FUSME	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.13	-	cyt	0					375
P55084 UniProt NPD GO	ECHB_HUMAN	Trifunctional enzyme subunit beta, mitochondrial precursor (TP-beta) [Includes: 3-ketoacyl-CoA thiol ...	0.13	-	mit	0	Mitochondrion	mitochondrial envelope [TAS]	609015		475
Q8HXX4 UniProt NPD GO	ECHB_MACFA	Trifunctional enzyme subunit beta, mitochondrial precursor (TP-beta) [Includes: 3-ketoacyl-CoA thiol ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				475
Q5R1W7 UniProt NPD GO	ECHB_PANTR	Trifunctional enzyme subunit beta, mitochondrial precursor (TP-beta) [Includes: 3-ketoacyl-CoA thiol ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				475
Q29428 UniProt NPD GO	TKDP1_SHEEP	Trophoblast Kunitz domain protein 1 precursor (TKDP-1)	0.13	-	exc	0	Secreted protein				265
Q5PQV5 UniProt NPD GO	TPBG_RAT	Trophoblast glycoprotein precursor (5T4 oncofetal trophoblast glycoprotein) (5T4 oncotrophoblast gly ...	0.13	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				426
Q9IAU2 UniProt NPD GO	GON8_RANDY	Trp-8 progonadoliberin precursor [Contains: Trp-8 gonadoliberin (Trp-8 gonadotropin-releasing hormon ...	0.13	-	gol	1 *	Secreted protein				90
P82408 UniProt NPD GO	ITR1_MOMCO	Trypsin inhibitor 1 (Trypsin inhibitor I) (MCoTI-I)	0.13	-	nuc	0	Secreted protein				34
Q38771 UniProt NPD GO	TBA_AVESA	Tubulin alpha chain	0.13	-	cyt	0					447
Q9ZRJ4 UniProt NPD GO	TBA_CHLVU	Tubulin alpha chain	0.13	-	cyt	0					451
Q06331 UniProt NPD GO	TBA_OCTDO	Tubulin alpha chain	0.13	-	cyt	0					451
P30436 UniProt NPD GO	TBA_ONCKE	Tubulin alpha chain	0.13	-	cyt	0					444
P33629 UniProt NPD GO	TBA_PRUDU	Tubulin alpha chain	0.13	-	cyt	0					450
P36220 UniProt NPD GO	TBA_TORMA	Tubulin alpha chain (Alpha T6)	0.13	-	cyt	0					451
Q5I2J3 UniProt NPD GO	TBA_GIBZE	Tubulin alpha chain (Alpha tubulin)	0.13	-	cyt	0					449
P33623 UniProt NPD GO	TBA1_ANEPH	Tubulin alpha-1 chain	0.13	-	cyt	0					451
P11139 UniProt NPD GO	TBA1_ARATH	Tubulin alpha-1 chain	0.13	-	cyt	0					450
P09204 UniProt NPD GO	TBA1_CHLRE	Tubulin alpha-1 chain	0.13	-	cyt	0					451
Q43473 UniProt NPD GO	TBA1_HORVU	Tubulin alpha-1 chain	0.13	-	cyt	0					450
P28752 UniProt NPD GO	TBA1_ORYSA	Tubulin alpha-1 chain	0.13	-	cyt	0					450
P46259 UniProt NPD GO	TBA1_PEA	Tubulin alpha-1 chain	0.13	-	cyt	0					452
O22347 UniProt NPD GO	TBA1_ELEIN	Tubulin alpha-1 chain (Alpha-1 tubulin)	0.13	-	cyt	0					451
P14640 UniProt NPD GO	TBA1_MAIZE	Tubulin alpha-1 chain (Alpha-1 tubulin)	0.13	-	cyt	0					451
P81948 UniProt NPD GO	TBA1_BOVIN	Tubulin alpha-1 chain (Alpha-tubulin 1)	0.13	-	cyt	0					448
P68367 UniProt NPD GO	TBA1_MACFA	Tubulin alpha-1 chain (Alpha-tubulin 1) (Testis-specific alpha-tubulin)	0.13	-	cyt	0					448
P68366 UniProt NPD GO	TBA1_HUMAN	Tubulin alpha-1 chain (Alpha-tubulin 1) (Testis-specific alpha-tubulin) (Tubulin H2-alpha)	0.13	-	cyt	0			191110		448
P11237 UniProt NPD GO	TBA1_NAEGR	Tubulin alpha-1/2/3 chain	0.13	-	cyt	0					453
P11481 UniProt NPD GO	TBA1_VOLCA	Tubulin alpha-1/alpha-2 chain	0.13	-	cyt	0					451
Q25563 UniProt NPD GO	TBA13_NAEGR	Tubulin alpha-13 chain	0.13	-	cyt	0					453
P49741 UniProt NPD GO	TBAA_SCHCO	Tubulin alpha-1A chain	0.13	-	cyt	0					448
Q53M52 UniProt NPD GO	TBA2_ORYSA	Tubulin alpha-2 chain	0.13	-	cyt	0					451
Q6VAG0 UniProt NPD GO	TBA2_GOSHI	Tubulin alpha-2 chain (Alpha-2 tubulin)	0.13	-	cyt	0					450
P14641 UniProt NPD GO	TBA2_MAIZE	Tubulin alpha-2 chain (Alpha-2 tubulin)	0.13	-	cyt	0					451
P33624 UniProt NPD GO	TBA2_ANEPH	Tubulin alpha-2 chain (Fragment)	0.13	-	nuc	0					364
Q9ZRR5 UniProt NPD GO	TBA3_HORVU	Tubulin alpha-3 chain	0.13	-	cyt	0					451
P09734 UniProt NPD GO	TBA3_YEAST	Tubulin alpha-3 chain	0.13	-	cyt	0		cytoplasmic microtubule [TAS] kinetochore microtubule [TAS] nuclear microtubule [TAS] polar microtubule [TAS] spindle pole body [IDA]			445
O22349 UniProt NPD GO	TBA3_ELEIN	Tubulin alpha-3 chain (Alpha-3 tubulin)	0.13	-	cyt	0					450
Q6VAF9 UniProt NPD GO	TBA4_GOSHI	Tubulin alpha-4 chain (Alpha-4 tubulin)	0.13	-	cyt	0					450
P68368 UniProt NPD GO	TBA4_MOUSE	Tubulin alpha-4 chain (Alpha-tubulin 4) (Alpha-tubulin isotype M-alpha-4)	0.13	-	cyt	0					448
P33627 UniProt NPD GO	TBA6_MAIZE	Tubulin alpha-6 chain (Alpha-6 tubulin)	0.13	-	cyt	0					450
P11833 UniProt NPD GO	TBB_PARLI	Tubulin beta chain (Beta tubulin)	0.13	-	cyt	0					447
P10878 UniProt NPD GO	TBB_TOXGO	Tubulin beta chain (Beta tubulin)	0.13	-	cyt	0					449
P02557 UniProt NPD GO	TBB_YEAST	Tubulin beta chain (Beta tubulin)	0.13	-	cyt	0		cytoplasmic microtubule [TAS] kinetochore microtubule [TAS] nuclear microtubule [TAS] polar microtubule [TAS] spindle pole body [IDA]			457
P33630 UniProt NPD GO	TBB1_ANEPH	Tubulin beta-1 chain (Beta-1 tubulin)	0.13	-	cyt	0					443
P18241 UniProt NPD GO	TBB1_BRUPA	Tubulin beta-1 chain (Beta-1 tubulin)	0.13	-	cyt	0					448
P37392 UniProt NPD GO	TBB1_LUPAL	Tubulin beta-1 chain (Beta-1 tubulin)	0.13	-	cyt	0	Cytoplasm				447

You are viewing entries 60551 to 60600 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.