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
P84507 UniProt NPD GO	TX1_CERCR	Toxin CcoTx1	0.08	-	nuc	0	Secreted protein	extracellular space [IDA]			33
P84508 UniProt NPD GO	TX2_CERCR	Toxin CcoTx2	0.08	-	nuc	0	Secreted protein	extracellular space [IDA]			33
P60273 UniProt NPD GO	MTX2_GRASP	Toxin GsMTx-2 (MTx2)	0.08	-	cyt	0	Secreted protein			1LUP	31
Q9P1P4 UniProt NPD GO	TAAR3_HUMAN	Trace amine-associated receptor 3 (G-protein coupled receptor 57)	0.08	-	end	6	Membrane; multi-pass membrane protein				343
Q7KQM2 UniProt NPD GO	TPPC5_PLAF7	Trafficking protein particle complex subunit 5 (41-2 protein antigen)	0.08	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity). Schizont membrane, internal surface of parasitiz ...				184
P15847 UniProt NPD GO	TPPC5_PLAFA	Trafficking protein particle complex subunit 5 (41-2 protein antigen)	0.08	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity). Schizont membrane, internal surface of parasitiz ...				184
Q5EU90 UniProt NPD GO	TER_EUGGR	Trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.44)	0.08	-	exc	1 *	Mitochondrion				539
Q9BZA1 UniProt NPD GO	TTY9A_HUMAN	Transcript Y 9A protein	0.08	-	nuc	1 *					69
Q02942 UniProt NPD GO	TRF_BLADI	Transferrin precursor	0.08	-	exc	0	Secreted protein				726
Q62351 UniProt NPD GO	TFR1_MOUSE	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.08	-	mit	1	Membrane; single-pass type II membrane protein (By similarity)	endosome [IDA] perinuclear region [IDA] plasma membrane [IDA]			763
Q8M9V4 UniProt NPD GO	IF1C_CHAGL	Translation initiation factor IF-1, chloroplast	0.08	-	nuc	0	Plastid; chloroplast				78
Q99LC8 UniProt NPD GO	EI2BA_MOUSE	Translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit alpha)	0.08	-	cyt	0					305
Q64270 UniProt NPD GO	EI2BA_RAT	Translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit alpha)	0.08	-	cyt	0					305
Q41009 UniProt NPD GO	TOC34_PEA	Translocase of chloroplast 34 (EC 3.6.5.-) (34 kDa chloroplast outer envelope protein) (GTP-binding ...	0.08	-	cyt	0	Plastid; chloroplast; chloroplast outer membrane			1H65	310
P45434 UniProt NPD GO	SSRA_ARATH	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.08	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				258
Q5E9E4 UniProt NPD GO	SSRB_BOVIN	Translocon-associated protein subunit beta precursor (TRAP-beta) (Signal sequence receptor subunit b ...	0.08	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				183
Q3V209 UniProt NPD GO	TMUB2_MOUSE	Transmembrane and ubiquitin-like domain-containing protein 2	0.08	-	end	3 *	Membrane; multi-pass membrane protein (Potential)			1WIA	319
P56982 UniProt NPD GO	TM14A_BOVIN	Transmembrane protein 14A	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				99
P56984 UniProt NPD GO	TM14A_PIG	Transmembrane protein 14A	0.08	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				99
Q9VVX5 UniProt NPD GO	NESSY_DROME	Transmembrane protein nessy	0.08	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			497
P55955 UniProt NPD GO	UP04_CAEEL	Transthyretin-like protein Y5F2A.1 precursor (Unknown spot 4 protein from 2D-page)	0.08	-	mit	0	Secreted protein				132
Q26255 UniProt NPD GO	PUR2_CHITE	Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase ...	0.08	-	nuc	0					1371
P49132 UniProt NPD GO	TPT_FLATR	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT)	0.08	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				407
P52178 UniProt NPD GO	TPT2_BRAOB	Triose phosphate/phosphate translocator, non-green plastid, chloroplast precursor (CTPT)	0.08	-	end	6	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				402
P81994 UniProt NPD GO	CRVP_TROCA	Tropirin (Fragment)	0.08	-	cyt	0	Secreted protein				27
Q9S747 UniProt NPD GO	ITR3_MOMCH	Trypsin inhibitor 3 (Trypsin inhibitor III) (MCTI-III)	0.08	-	nuc	0	Secreted protein				30
P84452 UniProt NPD GO	ITR5_SECED	Trypsin inhibitor 5 (Trypsin inhibitor V) (SETI-V)	0.08	-	nuc	0	Secreted protein				27
P35038 UniProt NPD GO	TRY4_ANOGA	Trypsin-4 precursor (EC 3.4.21.4)	0.08	-	vac	1 *	Secreted protein				275
Q15661 UniProt NPD GO	TRYB1_HUMAN	Tryptase beta-1 precursor (EC 3.4.21.59) (Tryptase-1) (Tryptase I)	0.08	-	end	0	Released from the secretory granules upon mast cell activation		191081		275
P20231 UniProt NPD GO	TRYB2_HUMAN	Tryptase beta-2 precursor (EC 3.4.21.59) (Tryptase-2) (Tryptase II)	0.08	-	end	0	Released from the secretory granules upon mast cell activation	extracellular region [NAS]		2GDD	275
P04688 UniProt NPD GO	TBA1_SCHPO	Tubulin alpha-1 chain	0.08	-	cyt	0		microtubule [TAS]			455
P52274 UniProt NPD GO	TBA8_CAEEL	Tubulin alpha-8 chain	0.08	-	cyt	0					452
Q3KVN1 UniProt NPD GO	TBB_CERBT	Tubulin beta chain (Beta tubulin)	0.08	-	cyt	0					447
Q24829 UniProt NPD GO	TBB_ENCHE	Tubulin beta chain (Beta tubulin)	0.08	-	cyt	0					439
P16040 UniProt NPD GO	TBB_ERYGR	Tubulin beta chain (Beta tubulin)	0.08	-	cyt	0					446
O42786 UniProt NPD GO	TBB_MYCPJ	Tubulin beta chain (Beta tubulin)	0.08	-	cyt	0	Cytoplasm				447
Q9LKI8 UniProt NPD GO	TBB_THAWE	Tubulin beta chain (Beta tubulin)	0.08	-	cyt	0					443
Q86ZP5 UniProt NPD GO	TBB_UNCNE	Tubulin beta chain (Beta tubulin)	0.08	-	cyt	0					447
P40904 UniProt NPD GO	TBB2_COLGL	Tubulin beta-2 chain (Beta-2 tubulin)	0.08	-	cyt	0					447
P22014 UniProt NPD GO	TBB2_COLGR	Tubulin beta-2 chain (Beta-2 tubulin)	0.08	-	cyt	0					447
Q3MHM5 UniProt NPD GO	TBB2C_BOVIN	Tubulin beta-2C chain	0.08	-	cyt	0					445
P68372 UniProt NPD GO	TBB2C_MOUSE	Tubulin beta-2C chain	0.08	-	cyt	0		tubulin [NAS]			445
P68371 UniProt NPD GO	TBB2C_HUMAN	Tubulin beta-2C chain (Tubulin beta-2 chain)	0.08	-	cyt	0			602660		445
Q3ZBU7 UniProt NPD GO	TBB4_BOVIN	Tubulin beta-4 chain	0.08	-	cyt	0					444
Q4R4X8 UniProt NPD GO	TBB4_MACFA	Tubulin beta-4 chain	0.08	-	cyt	0					444
Q9D6F9 UniProt NPD GO	TBB4_MOUSE	Tubulin beta-4 chain	0.08	-	cyt	0		cilium [IDA]			444
P04350 UniProt NPD GO	TBB4_HUMAN	Tubulin beta-4 chain (Tubulin 5 beta)	0.08	-	cyt	0			602662		444
Q9Y703 UniProt NPD GO	TBCA_SCHPO	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (Altered polarity protein 31)	0.08	-	nuc	0					119
P59684 UniProt NPD GO	TNFA_BOSIN	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				234
Q8WNR1 UniProt NPD GO	TNFA_DELLE	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233

You are viewing entries 69151 to 69200 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.