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
P07766 UniProt NPD GO	CD3E_HUMAN	T-cell surface glycoprotein CD3 epsilon chain precursor (T-cell surface antigen T3/Leu-4 epsilon cha ...	0.13	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [NAS] plasma membrane [IDA] T cell receptor complex [NAS]	186830	1XIW	207
Q28074 UniProt NPD GO	CD3G_BOVIN	T-cell surface glycoprotein CD3 gamma chain precursor (T-cell receptor T3 gamma chain)	0.13	-	end	2 *	Membrane; single-pass type I membrane protein				173
P31041 UniProt NPD GO	CD28_MOUSE	T-cell-specific surface glycoprotein CD28 precursor	0.13	-	mit	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [ISS]			218
P31042 UniProt NPD GO	CD28_RAT	T-cell-specific surface glycoprotein CD28 precursor	0.13	-	mit	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] lipid raft [IDA]			218
O94501 UniProt NPD GO	TCPA_SCHPO	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.13	-	cyt	0	Cytoplasm (By similarity)				556
Q3ZBH0 UniProt NPD GO	TCPB_BOVIN	T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)	0.13	-	cyt	0	Cytoplasm (By similarity)				534
Q2T9X2 UniProt NPD GO	TCPD_BOVIN	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.13	-	cyt	0	Cytoplasm (By similarity)				541
Q7TPB1 UniProt NPD GO	TCPD_RAT	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.13	-	cyt	0	Cytoplasm				538
P50991 UniProt NPD GO	TCPD_HUMAN	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta) (Stimulator of TAR RNA-binding)	0.13	-	cyt	0	Cytoplasm	cytoplasm [NAS]	605142		538
P80316 UniProt NPD GO	TCPE_MOUSE	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.13	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA]			541
O94515 UniProt NPD GO	TCPZ_SCHPO	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta)	0.13	-	cyt	0	Cytoplasm (By similarity)				535
Q00609 UniProt NPD GO	CD80_MOUSE	T-lymphocyte activation antigen CD80 precursor (Activation B7-1 antigen) (B7)	0.13	-	end	1	Membrane; single-pass type I membrane protein				306
Q9P0N9 UniProt NPD GO	TBCD7_HUMAN	TBC1 domain family member 7	0.13	-	nuc	0					293
P56841 UniProt NPD GO	TCLB2_MOUSE	TCL1B2 protein	0.13	-	cyt	0					117
Q95J79 UniProt NPD GO	TYOBP_BOVIN	TYRO protein tyrosine kinase-binding protein precursor (DNAX-activation protein 12)	0.13	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				108
P18252 UniProt NPD GO	TAC3_TACGI	Tachyplesin-3 (Tachyplesin III)	0.13	-		0	Secreted protein				17
Q6PZD2 UniProt NPD GO	TPSN_CERAE	Tapasin precursor (TPSN) (TPN) (TAP-binding protein)	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Probable ...				448
Q9Z0R8 UniProt NPD GO	TS1R1_RAT	Taste receptor type 1 member 1 precursor (G-protein coupled receptor 70)	0.13	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IC]			840
Q717C2 UniProt NPD GO	TS1R3_PANTR	Taste receptor type 1 member 3 precursor (Sweet taste receptor T1R3)	0.13	-	end	7	Membrane; multi-pass membrane protein				852
Q7TQA5 UniProt NPD GO	T2R39_MOUSE	Taste receptor type 2 member 39 (T2R39) (mT2R34)	0.13	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			319
Q68IP5 UniProt NPD GO	CX54B_CONMR	Tau conotoxin mr5.4b precursor (Fragment)	0.13	-	exc	0	Secreted protein (By similarity)				54
P27654 UniProt NPD GO	TIP1_YEAST	Temperature shock-inducible protein 1 precursor (EC 3.1.1.-)	0.13	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			210
Q7TQN2 UniProt NPD GO	TX101_CRIGR	Testis-expressed protein 101 precursor (Lipid raft-associated glycoprotein TEC-21)	0.13	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor Associated with lipid rafts (By similarity)				253
Q6VTH5 UniProt NPD GO	TSGA2_CYPCA	Testis-specific gene A2-like protein (Meichroacidin-like sperm-specific axonemal protein) (Meichroac ...	0.13	-	cyt	0	Localizes to the basal body and flagellum of mature spermatozoa				218
Q9LX31 UniProt NPD GO	GUN4_ARATH	Tetrapyrrole-binding protein, chloroplast precursor (Genomes uncoupled 4)	0.13	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Might be bound to membranes ...				265
Q9H1Z9 UniProt NPD GO	TSN10_HUMAN	Tetraspanin-10 (Tspan-10) (Oculospanin)	0.13	-	end	3	Membrane; multi-pass membrane protein (Potential)				355
P55788 UniProt NPD GO	THAN_PODMA	Thanatin	0.13	-	nuc	0	Secreted protein			8TFV	21
P35202 UniProt NPD GO	THI80_YEAST	Thiamine pyrophosphokinase (EC 2.7.6.2) (TPK) (Thiamine kinase)	0.13	-	cyt	0		cytoplasm [IDA]		1IG0	319
Q9BU02 UniProt NPD GO	THTPA_HUMAN	Thiamine-triphosphatase (EC 3.6.1.28) (ThTPase)	0.13	-	cyt	0	Cytoplasm	soluble fraction [NAS]			229
Q8C0L0 UniProt NPD GO	TXD13_MOUSE	Thioredoxin domain-containing protein 13 precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)				335
Q9FG36 UniProt NPD GO	TRXL5_ARATH	Thioredoxin-like 5, chloroplast precursor	0.13	-	cyt	0	Plastid; chloroplast (Potential)				185
P16120 UniProt NPD GO	THRC_YEAST	Threonine synthase (EC 4.2.3.1) (TS)	0.13	-	mit	0		cytoplasm [IDA] nucleus [IDA]		1KL7	514
P04047 UniProt NPD GO	KITH_CHICK	Thymidine kinase, cytosolic (EC 2.7.1.21)	0.13	-	cyt	0	Cytoplasm				224
P19971 UniProt NPD GO	TYPH_HUMAN	Thymidine phosphorylase precursor (EC 2.4.2.4) (TdRPase) (TP) (Platelet-derived endothelial cell gro ...	0.13	-	nuc	0			131222	1UOU	482
P07607 UniProt NPD GO	TYSY_MOUSE	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.13	-	cyt	0					307
Q9TT35 UniProt NPD GO	THBG_PIG	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.13	-	end	0	Secreted protein				412
P35577 UniProt NPD GO	THBG_RAT	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.13	-	end	0	Secreted protein	extracellular space [TAS]			418
Q90419 UniProt NPD GO	TWHH_BRARE	Tiggy-winkle hedgehog protein precursor (TWHH) (Sonic hedgehog B protein) (SHHB) [Contains: Tiggy-wi ...	0.13	-	cyt	1 *	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				416
Q9GNN8 UniProt NPD GO	CTXA_CARAL	Toxin A precursor (CaTX-A)	0.13	-	end	0	Secreted protein. Found in nematocyst				463
P20798 UniProt NPD GO	TXP1_PYETR	Toxin TxP-I precursor (Tox34)	0.13	-	nuc	0	Secreted protein				279
Q923Y4 UniProt NPD GO	TAA7H_RAT	Trace amine-associated receptor 7h (Trace amine receptor 6) (TaR-6)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				358
Q9BZ98 UniProt NPD GO	TTY12_HUMAN	Transcript Y 12 protein	0.13	-	cyt	0					90
Q9BXH5 UniProt NPD GO	TTY6_HUMAN	Transcript Y 6 protein	0.13	-	nuc	0					95
Q9TL25 UniProt NPD GO	IF1C_NEPOL	Translation initiation factor IF-1, chloroplast	0.13	-	cyt	0	Plastid; chloroplast				77
Q9D1D4 UniProt NPD GO	TMEDA_MOUSE	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (21 kDa tra ...	0.13	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side (By similarity)	integral to membrane [ISS] microsome [ISS] zymogen granule membrane [ISS]			219
Q9Y3Q3 UniProt NPD GO	TMED3_HUMAN	Transmembrane emp24 domain-containing protein 3 precursor (Membrane protein p24B)	0.13	-	end	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				217
Q6AXN3 UniProt NPD GO	TMED5_RAT	Transmembrane emp24 domain-containing protein 5 precursor	0.13	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				229
Q6AYQ4 UniProt NPD GO	TM109_RAT	Transmembrane protein 109 precursor (Mitsugumin-23) (Mg23)	0.13	+	end	5 *	Nucleus; nuclear outer membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum; ...				243
Q5EAU3 UniProt NPD GO	TM55A_XENLA	Transmembrane protein 55A (EC 3.1.3.-) (Type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.13	-	mit	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				256
O35587 UniProt NPD GO	TMEDA_MESAU	Transmembrane protein Tmp21 precursor (21 kDa transmembrane-trafficking protein) (Integral membrane ...	0.13	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side				219

You are viewing entries 60501 to 60550 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.