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
Q95LI5 UniProt NPD GO	CD3E_MACFA	T-cell surface glycoprotein CD3 epsilon chain precursor	0.24	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				198
Q717B2 UniProt NPD GO	TDPZ2_MOUSE	TD and POZ domain-containing protein 2	0.24	-	cyt	0					364
Q8CCM6 UniProt NPD GO	TI21L_MOUSE	TIM21-like protein, mitochondrial precursor	0.24	-	mit	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)				249
Q7TQB9 UniProt NPD GO	TR143_MOUSE	Taste receptor type 2 member 143 (T2R143) (Taste receptor type 2 member 43) (T2R43) (mT2R36)	0.24	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			293
Q41594 UniProt NPD GO	TASY_TAXBR	Taxadiene synthase (EC 4.2.3.17) (Taxa-4(5),11(12)-diene synthase)	0.24	-	cyt	0					862
Q2MV57 UniProt NPD GO	TECT2_MOUSE	Tectonic-2 precursor	0.24	-	end	0	Membrane; single-pass type I membrane protein (Potential)				700
Q92358 UniProt NPD GO	BQT1_SCHPO	Telomere bouquet protein 1 (Meiotic chromosome segregation protein bqt1) (Meiotically up-regulated p ...	0.24	-	cyt	0	Nucleus. Spindle pole body. Colocalizes with the telomere cluster during the 'horsetail' stage and t ...				132
Q08629 UniProt NPD GO	TICN1_HUMAN	Testican-1 precursor (Protein SPOCK)	0.24	-	nuc	0	Secreted protein; extracellular space; extracellular matrix		602264		439
Q62288 UniProt NPD GO	TICN1_MOUSE	Testican-1 precursor (Protein SPOCK)	0.24	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				442
Q96QS1 UniProt NPD GO	TSN32_HUMAN	Tetraspanin-32 (Protein Phemx)	0.24	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	603853		320
Q9BS26 UniProt NPD GO	TXND4_HUMAN	Thioredoxin domain-containing protein 4 precursor (Endoplasmic reticulum resident protein ERp44)	0.24	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [IDA] endoplasmic reticulum membrane [IDA] ER-Golgi intermediate compartment [IDA]	609170		406
Q8IYQ7 UniProt NPD GO	THNSL_HUMAN	Threonine synthase-like 1	0.24	-	cyt	0					743
P06579 UniProt NPD GO	TRBM_BOVIN	Thrombomodulin (TM) (Fetomodulin) (CD141 antigen) (Fragment)	0.24	-	nuc	1	Membrane; single-pass type I membrane protein				356
Q5XHZ9 UniProt NPD GO	TRP13_RAT	Thyroid receptor-interacting protein 13 (Thyroid hormone receptor interactor 13) (Trip-13)	0.24	-	cyt	0					432
Q8JGT9 UniProt NPD GO	CRVP_RHATT	Tigrin precursor	0.24	-	exc	0	Secreted protein				237
Q9GV72 UniProt NPD GO	CTX1_CARRA	Toxin 1 precursor (CrTX-A / CrTX-B)	0.24	+	nuc	0	Secreted protein. Found in nematocyst				450
Q8W0W3 UniProt NPD GO	TF2B_ORYSA	Transcription initiation factor IIB (General transcription factor TFIIB)	0.24	-	nuc	0	Nucleus				312
O13749 UniProt NPD GO	TF2B_SCHPO	Transcription initiation factor IIB (General transcription factor TFIIB)	0.24	-	nuc	0	Nucleus (By similarity)				340
Q95GN3 UniProt NPD GO	IF1C_CERJA	Translation initiation factor IF-1, chloroplast	0.24	-	nuc	0	Plastid; chloroplast				77
Q9MUU7 UniProt NPD GO	IF1C_MESVI	Translation initiation factor IF-1, chloroplast	0.24	-	cyt	0	Plastid; chloroplast				74
P70541 UniProt NPD GO	EI2BG_RAT	Translation initiation factor eIF-2B subunit gamma (eIF-2B GDP-GTP exchange factor subunit gamma)	0.24	-	cyt	0					452
Q6CLZ9 UniProt NPD GO	SEC62_KLULA	Translocation protein SEC62	0.24	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				246
Q9BVK6 UniProt NPD GO	TMED9_HUMAN	Transmembrane emp24 domain-containing protein 9 precursor (Glycoprotein 25L2)	0.24	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	ER-Golgi intermediate compartment [IDA]			214
O14669 UniProt NPD GO	TMG2_HUMAN	Transmembrane gamma-carboxyglutamic acid protein 2 precursor (Proline-rich Gla protein 2) (Proline-r ...	0.24	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604429		202
Q5R491 UniProt NPD GO	TMM66_PONPY	Transmembrane protein 66 precursor	0.24	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				339
Q96BY9 UniProt NPD GO	TMM66_HUMAN	Transmembrane protein 66 precursor (Protein FOAP-7) (HBV X-transactivated gene 3 protein)	0.24	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				339
Q9JJR8 UniProt NPD GO	TMM9B_MOUSE	Transmembrane protein 9B precursor	0.24	-	end	2 *	Membrane; single-pass membrane protein (Potential)				199
P81995 UniProt NPD GO	CRVP_TRIPP	Tripurin (Fragment)	0.24	-	nuc	0	Secreted protein				33
P01073 UniProt NPD GO	ITRY_MAIZE	Trypsin inhibitor	0.24	-	nuc	0					65
O59837 UniProt NPD GO	TBB_PHYCI	Tubulin beta chain (Beta tubulin)	0.24	-	cyt	0					444
P32924 UniProt NPD GO	TBB1_GEOCN	Tubulin beta-1 chain (Beta-1 tubulin)	0.24	-	cyt	0					447
Q39697 UniProt NPD GO	TBB2_DAUCA	Tubulin beta-2 chain (Beta-2 tubulin)	0.24	-	cyt	0					444
Q8WP13 UniProt NPD GO	TBB4Q_PAPHA	Tubulin beta-4q chain	0.24	-	cyt	0					444
P34475 UniProt NPD GO	TBG_CAEEL	Tubulin gamma chain (Gamma tubulin)	0.24	-	cyt	0		centrosome [IDA]			444
Q32KS0 UniProt NPD GO	TBCE_BOVIN	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.24	-	nuc	0					528
Q9NUY9 UniProt NPD GO	TDRD4_HUMAN	Tudor domain-containing protein 4	0.24	-	cyt	0					633
Q9D8D0 UniProt NPD GO	TR13C_MOUSE	Tumor necrosis factor receptor superfamily member 13C (B cell-activating factor receptor) (BAFF rece ...	0.24	-	nuc	1	Membrane; single-pass type III membrane protein (Probable)	external side of plasma membrane [IDA]			175
P50284 UniProt NPD GO	TNR3_MOUSE	Tumor necrosis factor receptor superfamily member 3 precursor (Lymphotoxin-beta receptor)	0.24	-	exc	1	Membrane; single-pass type I membrane protein				415
Q9SB04 UniProt NPD GO	ARR5_ARATH	Two-component response regulator ARR5 (Response reactor 2)	0.24	-	nuc	0	Nucleus (Probable)				184
Q9Z1Y9 UniProt NPD GO	IOD2_MOUSE	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.24	-	nuc	0					262
Q9H3Y6 UniProt NPD GO	SRMS_HUMAN	Tyrosine-protein kinase Srms (EC 2.7.10.2)	0.24	-	mit	0					488
O02373 UniProt NPD GO	UGDH_DROME	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH) (Protein suga ...	0.24	-	cyt	0					476
O97420 UniProt NPD GO	CI016_DROME	UPF0184 protein CG14818	0.24	-	nuc	0					96
P00126 UniProt NPD GO	UCRH_BOVIN	Ubiquinol-cytochrome c reductase complex 11 kDa protein, mitochondrial precursor (EC 1.10.2.2) (Mito ...	0.24	-	nuc	0	Mitochondrion; mitochondrial inner membrane			3BCC	91
Q871K1 UniProt NPD GO	UCR7_NEUCR	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.24	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				123
Q96AX9 UniProt NPD GO	MIB2_HUMAN	Ubiquitin ligase protein MIB2 (EC 6.3.2.-) (Mind bomb homolog 2) (Zinc finger ZZ type with ankyrin r ...	0.24	-	nuc	0	Cytoplasm. Endosome. Colocalizes with endosomal compartments				1013
P50876 UniProt NPD GO	UB7I4_HUMAN	Ubiquitin-conjugating enzyme 7-interacting protein 4 (UbcM4-interacting protein 4) (RING finger prot ...	0.24	-	cyt	1	Nucleus (By similarity)	Golgi apparatus [IDA]		1WIM	292
P61077 UniProt NPD GO	UB2D3_HUMAN	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) (Ubiquitin-protein ligase D3) (Ubiquitin carrier pr ...	0.24	-	nuc	0			602963	2FUH	147
P61079 UniProt NPD GO	UB2D3_MOUSE	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) (Ubiquitin-protein ligase D3) (Ubiquitin carrier pr ...	0.24	-	nuc	0					147
P61078 UniProt NPD GO	UB2D3_RAT	Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) (Ubiquitin-protein ligase D3) (Ubiquitin carrier pr ...	0.24	-	nuc	0					147

You are viewing entries 46901 to 46950 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.