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
Q9BX59 UniProt NPD GO	TPSNR_HUMAN	Tapasin-related protein precursor (TAPASIN-R) (Tapasin-like) (TAP-binding protein-related protein) ( ...	0.25	-	nuc	1	Cell membrane; single-pass type I membrane protein (Probable). Endoplasmic reticulum; endoplasmic re ...		607081		468
Q646F4 UniProt NPD GO	T2R14_PAPHA	Taste receptor type 2 member 14 (T2R14)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				319
Q645T6 UniProt NPD GO	T2R50_MACMU	Taste receptor type 2 member 50 (T2R50)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646E4 UniProt NPD GO	T2R50_PANPA	Taste receptor type 2 member 50 (T2R50)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646C3 UniProt NPD GO	T2R50_PANTR	Taste receptor type 2 member 50 (T2R50)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646G2 UniProt NPD GO	T2R50_PAPHA	Taste receptor type 2 member 50 (T2R50)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				299
Q2QL92 UniProt NPD GO	TES_MICMU	Testin	0.25	-	nuc	0					421
P47226 UniProt NPD GO	TES_MOUSE	Testin (TES1/TES2)	0.25	-	nuc	0					423
Q9CR81 UniProt NPD GO	TEX12_MOUSE	Testis-expressed sequence 12 protein	0.25	-	nuc	0					123
P70675 UniProt NPD GO	TSX_MOUSE	Testis-specific protein TSX	0.25	-	nuc	0					144
Q8N0Z6 UniProt NPD GO	TTC5_HUMAN	Tetratricopeptide repeat protein 5 (TPR repeat protein 5)	0.25	-	cyt	0					440
Q90501 UniProt NPD GO	TBFA_EPTST	Thread biopolymer filament subunit alpha	0.25	-	cyt	2	Secreted protein; extracellular space				643
O74267 UniProt NPD GO	GLY1_ASHGO	Threonine aldolase (EC 4.1.2.5)	0.25	-	cyt	0					382
Q9BH05 UniProt NPD GO	THNSL_MACFA	Threonine synthase-like 1	0.25	-	cyt	0					743
Q9NQE7 UniProt NPD GO	TSSP_HUMAN	Thymus-specific serine protease precursor (EC 3.4.-.-)	0.25	-	vac	1 *	Cytoplasmic vesicle. Vesicular, either lysosomal or endosomal		607169		514
Q28198 UniProt NPD GO	TPA_BOVIN	Tissue-type plasminogen activator precursor (EC 3.4.21.68) (tPA) (t-PA) (t-plasminogen activator) [C ...	0.25	-	exc	0	Secreted protein; extracellular space				566
Q9H497 UniProt NPD GO	TOR3A_HUMAN	Torsin-3A precursor (Torsin family 3 member A) (ATP-dependent interferon-responsive protein)	0.25	-	exc	0	Cytoplasm. Endoplasmic reticulum		607555		397
O88968 UniProt NPD GO	TCO2_MOUSE	Transcobalamin-2 precursor (Transcobalamin II) (TCII) (TC II)	0.25	-	end	0	Secreted protein				430
Q15370 UniProt NPD GO	ELOB_HUMAN	Transcription elongation factor B polypeptide 2 (RNA polymerase II transcription factor SIII subunit ...	0.25	-	nuc	0	Nucleus (Probable)		600787	2C9W	118
P62869 UniProt NPD GO	ELOB_MOUSE	Transcription elongation factor B polypeptide 2 (RNA polymerase II transcription factor SIII subunit ...	0.25	-	nuc	0	Nucleus (Probable)			2FNJ	118
P62870 UniProt NPD GO	ELOB_RAT	Transcription elongation factor B polypeptide 2 (RNA polymerase II transcription factor SIII subunit ...	0.25	-	nuc	0	Nucleus (Probable)				118
Q12870 UniProt NPD GO	TCF15_HUMAN	Transcription factor 15 (bHLH-EC2 protein) (Paraxis)	0.25	+	nuc	0	Nucleus (By similarity)		601010		199
Q13891 UniProt NPD GO	BT3L2_HUMAN	Transcription factor BTF3 homolog 2 (Basic transcription factor 3-like 2)	0.25	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	603738		67
O73742 UniProt NPD GO	COE3_XENLA	Transcription factor COE3 (xCOE3) (Olf-1/EBF-like 2) (OE-2) (xOE-2) (xEBF-3)	0.25	-	nuc	0	Nucleus (Potential)				598
Q9LK95 UniProt NPD GO	MYB21_ARATH	Transcription factor MYB21 (Myb-related protein 21) (AtMYB21) (Myb homolog 3) (AtMyb3)	0.25	-	nuc	0	Nucleus (Probable)				226
Q9U5W9 UniProt NPD GO	TAF10_DROME	Transcription initiation factor TFIID subunit 10 (Transcription initiation factor TFIID 24 kDa subun ...	0.25	-	nuc	0	Cytoplasm. Nucleus	SAGA complex [IPI] transcription factor TFIID complex [IDA]			167
O74319 UniProt NPD GO	TAF73_SCHPO	Transcription initiation factor TFIID subunit taf73 (Transcription initiation factor TFIID 73 kDa su ...	0.25	-	cyt	0	Nucleus (By similarity)	transcription factor TFIID complex [TAS]			642
Q9UUG8 UniProt NPD GO	TUP12_SCHPO	Transcriptional repressor tup12	0.25	-	mit	0		nucleus [IDA]			586
Q32RV0 UniProt NPD GO	IF1C_STAPU	Translation initiation factor IF-1, chloroplast	0.25	-	nuc	0	Plastid; chloroplast				84
Q3E764 UniProt NPD GO	TMA7_YEAST	Translation machinery-associated protein 7	0.25	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			64
Q9BVT8 UniProt NPD GO	TMUB1_HUMAN	Transmembrane and ubiquitin-like domain-containing protein 1 (Ubiquitin-like protein SB144)	0.25	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				246
Q99KF1 UniProt NPD GO	TMED9_MOUSE	Transmembrane emp24 domain-containing protein 9 precursor (Glycoprotein 25L2)	0.25	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				214
Q8NEW7 UniProt NPD GO	TMIE_HUMAN	Transmembrane inner ear expressed protein precursor	0.25	+	end	2 *	Membrane; single-pass type I membrane protein (Potential)		607237		155
Q8K467 UniProt NPD GO	TMIE_MOUSE	Transmembrane inner ear expressed protein precursor	0.25	+	end	2 *	Membrane; single-pass type I membrane protein (Potential)				153
Q66I51 UniProt NPD GO	T55BB_BRARE	Transmembrane protein 55B-B (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase ...	0.25	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				262
Q9JLT2 UniProt NPD GO	TREA_MOUSE	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.25	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	brush border [TAS]			576
Q13641 UniProt NPD GO	TPBG_HUMAN	Trophoblast glycoprotein precursor (5T4 oncofetal trophoblast glycoprotein) (5T4 oncotrophoblast gly ...	0.25	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	190920		420
P0C171 UniProt NPD GO	TIP39_BOVIN	Tuberoinfundibular peptide of 39 residues precursor (TIP39)	0.25	-	mit	1 *	Secreted protein				100
Q96A98 UniProt NPD GO	TIP39_HUMAN	Tuberoinfundibular peptide of 39 residues precursor (TIP39)	0.25	-	mit	1 *	Secreted protein		608386		100
Q39445 UniProt NPD GO	TBB_CICAR	Tubulin beta chain (Beta tubulin)	0.25	-	cyt	0					449
P04107 UniProt NPD GO	TBB_TRYBR	Tubulin beta chain (Beta tubulin)	0.25	-	cyt	0					442
P38585 UniProt NPD GO	TTL_MOUSE	Tubulin--tyrosine ligase (EC 6.3.2.25) (TTL)	0.25	-	cyt	0		microtubule [IC]			377
P32972 UniProt NPD GO	TNFL8_MOUSE	Tumor necrosis factor ligand superfamily member 8 (CD30 ligand) (CD30-L) (CD153 antigen)	0.25	-	nuc	1 *	Membrane; single-pass type II membrane protein				239
Q9NP84 UniProt NPD GO	TNR12_HUMAN	Tumor necrosis factor receptor superfamily member 12A precursor (Fibroblast growth factor-inducible ...	0.25	-	end	2 *	Membrane; single-pass type I membrane protein		605914		129
P15725 UniProt NPD GO	TNR4_RAT	Tumor necrosis factor receptor superfamily member 4 precursor (OX40L receptor) (OX40 antigen) (MRC O ...	0.25	-	end	1	Membrane; single-pass type I membrane protein				271
P55327 UniProt NPD GO	TPD52_HUMAN	Tumor protein D52 (N8 protein)	0.25	-	nuc	0		cytoplasm [IDA] endoplasmic reticulum [IDA] perinuclear region [IDA]	604068		184
P16422 UniProt NPD GO	TACD1_HUMAN	Tumor-associated calcium signal transducer 1 precursor (Major gastrointestinal tumor-associated prot ...	0.25	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	185535		314
P08103 UniProt NPD GO	HCK_MOUSE	Tyrosine-protein kinase HCK (EC 2.7.10.2) (p56-HCK/p59-HCK) (Hemopoietic cell kinase) (B-cell/myeloi ...	0.25	-	nuc	0	Isoform p59-HCK, isoform p56-HCK: Membrane; lipid-anchor. Isoform p59-HCK: Cytoplasm				523
P97710 UniProt NPD GO	SHPS1_RAT	Tyrosine-protein phosphatase non-receptor type substrate 1 precursor (SHP substrate 1) (SHPS-1) (Inh ...	0.25	-	exc	1	Membrane; single-pass type I membrane protein				509
P97797 UniProt NPD GO	SHPS1_MOUSE	Tyrosine-protein phosphatase non-receptor type substrate 1 precursor (SHP substrate 1) (SHPS-1) (Inh ...	0.25	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IDA]			513

You are viewing entries 45801 to 45850 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.