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
P19118 UniProt NPD GO	TPIS_NICPL	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.02	-		0	Cytoplasm (Probable)				10
P81666 UniProt NPD GO	TPIS_PINPS	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragments)	0.02	-		0	Cytoplasm (Probable)				17
P04789 UniProt NPD GO	TPIS_TRYBB	Triosephosphate isomerase, glycosomal (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0	Glycosome			6TIM	250
P29289 UniProt NPD GO	TNNC1_HOMAM	Troponin C, isoform 1	0.02	-	cyt	0					150
P29291 UniProt NPD GO	TNNCB_HOMAM	Troponin C, isoform 2B	0.02	-	cyt	0					150
P06708 UniProt NPD GO	TNNC2_PONLE	Troponin C, isotype gamma	0.02	-	cyt	0					150
P39040 UniProt NPD GO	TYTR_CRIFA	Trypanothione reductase (EC 1.8.1.12) (TR) (N(1),N(8)-bis(glutathionyl)spermidine reductase)	0.02	-	cyt	0	Cytoplasm			2TPR	491
P39050 UniProt NPD GO	TYTR_LEIDO	Trypanothione reductase (EC 1.8.1.12) (TR) (N(1),N(8)-bis(glutathionyl)spermidine reductase)	0.02	-	mit	0	Cytoplasm				491
P29787 UniProt NPD GO	TRY5_AEDAE	Trypsin 5G1 precursor (EC 3.4.21.4) (Fragment)	0.02	-	cyt	0	Secreted protein; extracellular space				238
P35005 UniProt NPD GO	TRYE_DROME	Trypsin epsilon precursor (EC 3.4.21.4)	0.02	-	vac	0	Secreted protein; extracellular space				256
P25850 UniProt NPD GO	ITR2_LUFCY	Trypsin inhibitor 2 (Trypsin inhibitor II) (LCTI-II)	0.02	-	nuc	0	Secreted protein				30
P32041 UniProt NPD GO	ITR3_CUCMC	Trypsin inhibitor 3 (Trypsin inhibitor III) (CMCTI-III) [Contains: Trypsin inhibitor 2 (Trypsin inhi ...	0.02	-	nuc	0	Secreted protein				30
Q9S8I2 UniProt NPD GO	ITR3_LUFCY	Trypsin inhibitor 3 (Trypsin inhibitor III) (LCTI-III)	0.02	-	nuc	0	Secreted protein				29
P83398 UniProt NPD GO	ITR7_CYCPE	Trypsin inhibitor 7 (Trypsin inhibitor VII) (CyPTI-VII)	0.02	-	nuc	0	Secreted protein				30
Q42328 UniProt NPD GO	ITI2_ARATH	Trypsin inhibitor ATTI-2 precursor (diDi 4T-1) (ATTp)	0.02	-	gol	1 *	Secreted protein (Potential)			1JXC	89
P09942 UniProt NPD GO	ID5B_ADEPA	Trypsin inhibitor DE5, beta chain	0.02	-	cyt	0					38
P70059 UniProt NPD GO	TRY2_XENLA	Trypsin precursor (EC 3.4.21.4)	0.02	-	exc	0	Secreted protein; extracellular space				244
P42278 UniProt NPD GO	TRYT_DROME	Trypsin theta precursor (EC 3.4.21.4)	0.02	-	exc	1 *	Secreted protein; extracellular space				262
P54630 UniProt NPD GO	TRYZ_DROER	Trypsin zeta precursor (EC 3.4.21.4)	0.02	-	exc	0	Secreted protein; extracellular space				281
P35041 UniProt NPD GO	TRY7_ANOGA	Trypsin-7 precursor (EC 3.4.21.4)	0.02	-	vac	0	Secreted protein				267
P41495 UniProt NPD GO	TMOF_SARBU	Trypsin-modulating oostatic factor (TMOF)	0.02	-		0					6
Q9QUL7 UniProt NPD GO	TRYG1_MOUSE	Tryptase gamma precursor (EC 3.4.21.-) (Transmembrane tryptase) [Contains: Tryptase gamma light chai ...	0.02	-	end	1	Membrane; single-pass membrane protein (Potential)				311
P16578 UniProt NPD GO	TRP_COPCI	Tryptophan synthase (EC 4.2.1.20)	0.02	-	cyt	0					702
Q3SZ26 UniProt NPD GO	WRB_BOVIN	Tryptophan-rich protein	0.02	-	end	3 *	Nucleus (By similarity)				174
Q8K0D7 UniProt NPD GO	WRB_MOUSE	Tryptophan-rich protein	0.02	-	end	3 *	Nucleus (By similarity)				174
P10489 UniProt NPD GO	TBA_LEPSE	Tubulin alpha chain (Fragment)	0.02	-	cyt	0					25
P38668 UniProt NPD GO	TBA1_NEUCR	Tubulin alpha-A chain	0.02	-	cyt	0					453
P05219 UniProt NPD GO	TBB_SCHPO	Tubulin beta chain (Beta tubulin)	0.02	-	cyt	0		microtubule [IDA]			448
P43488 UniProt NPD GO	TNFL4_MOUSE	Tumor necrosis factor ligand superfamily member 4 (OX40 ligand) (OX40L) (CD252 antigen)	0.02	-	cyt	0	Membrane; single-pass type II membrane protein				198
P23383 UniProt NPD GO	TNFA_SHEEP	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.02	-	cyt	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				234
O75896 UniProt NPD GO	TUSC2_HUMAN	Tumor suppressor candidate 2 (PDGFA-associated protein 2) (Fus-1 protein) (Fusion 1 protein)	0.02	-	cyt	0			607052		109
Q9WVF8 UniProt NPD GO	TUSC2_MOUSE	Tumor suppressor candidate 2 (PDGFA-associated protein 2) (Fus-1 protein) (Fusion 1 protein)	0.02	-	cyt	0					109
Q9SHC2 UniProt NPD GO	ARR16_ARATH	Two-component response regulator ARR16	0.02	-	nuc	0	Nucleus (Probable)				164
P56626 UniProt NPD GO	RIP1_TRIAN	Type I ribosome-inactivating protein trichoanguina precursor (EC 3.2.2.22) (rRNA N-glycosidase) (RIP ...	0.02	-	end	0					294
P32303 UniProt NPD GO	AGTRL_XENLA	Type-1-like angiotensin II receptor 1 (AT1)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				362
P12417 UniProt NPD GO	ANP2_ANALU	Type-3 ice-structuring protein 1.5 precursor (ISP 3) (Antifreeze protein type III)	0.02	-	vac	0					88
P12416 UniProt NPD GO	ANP1_ANALU	Type-3 ice-structuring protein 1.9 precursor (ISP 3) (Antifreeze protein type III)	0.02	-	vac	0					88
Q8RY79 UniProt NPD GO	TYDC1_ARATH	Tyrosine decarboxylase 1 (EC 4.1.1.25)	0.02	-	nuc	0					490
P42689 UniProt NPD GO	SRK3_SPOLA	Tyrosine-protein kinase SRK3 (EC 2.7.10.2) (Fragment)	0.02	-	cyt	0	Cytoplasm (Probable)				334
O94408 UniProt NPD GO	LSM2_SCHPO	U6 snRNA-associated Sm-like protein LSm2	0.02	-	cyt	0	Nucleus (By similarity)				96
Q5KLF2 UniProt NPD GO	ALG13_CRYNE	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.02	-	exc	0	Endoplasmic reticulum (By similarity)				200
Q00974 UniProt NPD GO	YEA4_KLULA	UDP-N-acetylglucosamine transporter YEA4 (Golgi UDP-GlcNAc transporter)	0.02	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				328
Q9H3H5 UniProt NPD GO	GPT_HUMAN	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.02	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		608093		408
Q9R0M8 UniProt NPD GO	S35A2_MOUSE	UDP-galactose translocator (UDP-galactose transporter) (UGT) (UDP-Gal-Tr) (Solute carrier family 35 ...	0.02	-	end	8 *	Membrane; multi-pass membrane protein	Golgi membrane [IDA]			390
P08541 UniProt NPD GO	UDB2_RAT	UDP-glucuronosyltransferase 2B2 precursor (EC 2.4.1.17) (UDPGT) (3-hydroxyandrogen specific) (UDPGTr ...	0.02	-	end	1	Microsome	intracellular cyclic nucleotide activated c... [IDA]			530
Q5SPF7 UniProt NPD GO	UN93A_BRARE	UNC93 homolog A	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				465
Q6DDL7 UniProt NPD GO	UN93A_XENLA	UNC93 homolog A	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				460
Q710D3 UniProt NPD GO	UN93A_MOUSE	UNC93 homolog A (UNC-93A protein)	0.02	-	end	10 *	Cell membrane; multi-pass membrane protein (By similarity)				458
Q86WB7 UniProt NPD GO	UN93A_HUMAN	UNC93 homolog A (UNC-93A protein) (HmUNC-93A)	0.02	-	end	12 *	Cell membrane; multi-pass membrane protein	integral to membrane [NAS] plasma membrane [IDA]	607995		457
P38301 UniProt NPD GO	YB37_YEAST	UPF0016 protein YBR187W	0.02	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			280

You are viewing entries 86051 to 86100 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.