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
Q63467 UniProt NPD GO	TFF1_RAT	Trefoil factor 1 precursor (pS2 protein)	0.04	-	exc	0	Secreted protein	cytoplasm [TAS]			81
Q03404 UniProt NPD GO	TFF2_MOUSE	Trefoil factor 2 precursor (Spasmolytic polypeptide) (SP)	0.04	-	exc	0	Secreted protein				129
Q9W2M2 UniProt NPD GO	TREA_DROME	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.04	-	exc	0		anchored to plasma membrane [ISS]			596
Q67ZU1 UniProt NPD GO	LIP2_ARATH	Triacylglycerol lipase 2 precursor (EC 3.1.1.3)	0.04	-	mit	1 *	Secreted protein (Probable)				418
P32089 UniProt NPD GO	TXTP_RAT	Tricarboxylate transport protein, mitochondrial precursor (Citrate transport protein) (CTP) (Tricarb ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				311
Q6A1B7 UniProt NPD GO	TRI5_TRIHA	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.04	-	cyt	0					388
P21872 UniProt NPD GO	PUR2_CHICK	Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase ...	0.04	-	cyt	0					1003
P29613 UniProt NPD GO	TPIS_DROME	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.04	-	cyt	0					247
Q7JNS1 UniProt NPD GO	TPIS_DROSI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.04	-	cyt	0					247
O77458 UniProt NPD GO	TPIS_DROYA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.04	-	cyt	0					247
P48499 UniProt NPD GO	TPIS_LEIME	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.04	-	cyt	0	Cytoplasm. Glycosome			1QDS	251
Q6C2T9 UniProt NPD GO	TPIS_YARLI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.04	-	cyt	0					247
P52270 UniProt NPD GO	TPIS_TRYCR	Triosephosphate isomerase, glycosomal (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.04	-	cyt	0	Glycosome			1TCD	251
Q09665 UniProt NPD GO	TNNC2_CAEEL	Troponin C, isoform 2	0.04	-	cyt	0					160
P81660 UniProt NPD GO	TNNC2_ANGAN	Troponin C, skeletal muscle (TNC)	0.04	-	cyt	0					160
P63315 UniProt NPD GO	TNNC1_BOVIN	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.04	-	cyt	0					161
P09860 UniProt NPD GO	TNNC1_CHICK	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.04	-	cyt	0				3CTN	161
P63316 UniProt NPD GO	TNNC1_HUMAN	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.04	-	cyt	0			191040	1WRL	161
P19123 UniProt NPD GO	TNNC1_MOUSE	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.04	-	cyt	0					161
P63317 UniProt NPD GO	TNNC1_PIG	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.04	-	cyt	0				1LJ6	161
P02591 UniProt NPD GO	TNNC1_RABIT	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.04	-	cyt	0					161
Q9W0Y1 UniProt NPD GO	TINA1_DROME	Troponin C-akin-1 protein	0.04	-	mit	0					167
Q01807 UniProt NPD GO	LEC2_MEDTR	Truncated lectin 2 precursor	0.04	-	exc	0					280
P28593 UniProt NPD GO	TYTR_TRYCR	Trypanothione reductase (EC 1.8.1.12) (TR) (N(1),N(8)-bis(glutathionyl)spermidine reductase)	0.04	-	cyt	0	Cytoplasm			1NDA	492
Q90627 UniProt NPD GO	TRY1_CHICK	Trypsin I-P1 precursor (EC 3.4.21.4)	0.04	-	exc	0	Secreted protein; extracellular space				248
Q90628 UniProt NPD GO	TRY2_CHICK	Trypsin I-P38 precursor (EC 3.4.21.4)	0.04	-	exc	0	Secreted protein; extracellular space				248
P12071 UniProt NPD GO	ITR2_ECBEL	Trypsin inhibitor 2 (Trypsin inhibitor II) (EETI-II)	0.04	-	nuc	0	Secreted protein			2LET	30
P09943 UniProt NPD GO	IDE3_ERYCA	Trypsin inhibitor DE-3	0.04	-	cyt	0				1TIE	172
P68171 UniProt NPD GO	IDE3_ERYLA	Trypsin inhibitor DE-3	0.04	-	cyt	0					172
P81366 UniProt NPD GO	IDE3_ERYVA	Trypsin inhibitor DE-3 (ETIA)	0.04	-	cyt	0					172
P24924 UniProt NPD GO	ITRY_ACACO	Trypsin inhibitor precursor [Contains: Trypsin inhibitor chain A; Trypsin inhibitor chain B]	0.04	-	cyt	0					176
P35036 UniProt NPD GO	TRY2_ANOGA	Trypsin-2 precursor (EC 3.4.21.4)	0.04	-	vac	1 *	Secreted protein				277
P35040 UniProt NPD GO	TRY6_ANOGA	Trypsin-6 precursor (EC 3.4.21.4)	0.04	-	vac	0	Secreted protein				273
P15944 UniProt NPD GO	TRYT_CANFA	Tryptase precursor (EC 3.4.21.59)	0.04	-	end	0	Released from the secretory granules upon mast cell activation				275
Q9N2D1 UniProt NPD GO	TRYT_PIG	Tryptase precursor (EC 3.4.21.59)	0.04	-	mit	0	Released from the secretory granules upon mast cell activation				275
P00931 UniProt NPD GO	TRP_YEAST	Tryptophan synthase (EC 4.2.1.20)	0.04	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			707
Q6B8L2 UniProt NPD GO	TRPA_GRATL	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.04	-	nuc	0	Plastid; chloroplast				268
P25269 UniProt NPD GO	TRBP2_ARATH	Tryptophan synthase beta chain 2, chloroplast precursor (EC 4.2.1.20)	0.04	-	mit	0	Plastid; chloroplast (Probable)				475
P84831 UniProt NPD GO	TY1_ASCTR	Tryptophyllin-1	0.04	-		0	Secreted protein	extracellular region [IDA]			7
P04096 UniProt NPD GO	TY13_PHYRO	Tryptophyllin-13	0.04	-		0	Secreted protein				13
P82065 UniProt NPD GO	TY51_LITRU	Tryptophyllin-5.1	0.04	-		0	Secreted protein				7
P50719 UniProt NPD GO	TBA_HAECO	Tubulin alpha chain	0.04	-	cyt	0					450
P02553 UniProt NPD GO	TBA_LYTPI	Tubulin alpha chain (Fragment)	0.04	-	cyt	0					161
P41742 UniProt NPD GO	TBB_AJECA	Tubulin beta chain (Beta tubulin)	0.04	-	cyt	0					445
P50259 UniProt NPD GO	TBB1_PORPU	Tubulin beta-1 chain (Beta-1 tubulin)	0.04	-	cyt	0					457
P59693 UniProt NPD GO	TNFA_BUBBU	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.04	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P51742 UniProt NPD GO	TNFA_CANFA	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.04	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P13296 UniProt NPD GO	TNFA_CAPHI	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.04	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				234
P16599 UniProt NPD GO	TNFA_RAT	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.04	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	extracellular space [TAS]			235
Q9GLN9 UniProt NPD GO	AGTR1_PANTR	Type-1 angiotensin II receptor (AT1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				359

You are viewing entries 78651 to 78700 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.