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
P87025 UniProt NPD GO	THR1_GLOLA	Trihydroxynaphthalene reductase (EC 1.1.1.-) (T3HN reductase)	0.01	-	cyt	0					272
Q10657 UniProt NPD GO	TPIS_CAEEL	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0				1MO0	247
Q9P940 UniProt NPD GO	TPIS_CANAL	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	mit	0	Cytoplasm				247
P00940 UniProt NPD GO	TPIS_CHICK	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0				8TIM	247
Q12574 UniProt NPD GO	TPIS_COPCI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	mit	0					251
P30741 UniProt NPD GO	TPIS_CULTA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0					246
P60174 UniProt NPD GO	TPIS_HUMAN	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0			190450	1WYI	248
P00941 UniProt NPD GO	TPIS_LATCH	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0					247
Q589R5 UniProt NPD GO	TPIS_ORYLA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0					248
P60175 UniProt NPD GO	TPIS_PANTR	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0					248
Q9C401 UniProt NPD GO	TPIS_ZYGBA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0					248
P92119 UniProt NPD GO	TPIS_AEDTO	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.01	-	cyt	0					206
P91895 UniProt NPD GO	TPIS_ANOME	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.01	-	cyt	0					206
Q9SKP6 UniProt NPD GO	TPIC_ARATH	Triosephosphate isomerase, chloroplast precursor (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	mit	0	Plastid; chloroplast (By similarity)				315
P12863 UniProt NPD GO	TPIS_MAIZE	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.01	-	cyt	0	Cytoplasm (Probable)				252
P48493 UniProt NPD GO	TPIS_LACSA	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.01	-	cyt	0	Cytoplasm (Probable)				195
P50163 UniProt NPD GO	TRN2_DATST	Tropinone reductase 2 (EC 1.1.1.236) (Tropinone reductase-II) (TR-II)	0.01	-	cyt	1				2AE2	260
P50164 UniProt NPD GO	TRN2_HYONI	Tropinone reductase 2 (EC 1.1.1.236) (Tropinone reductase-II) (TR-II)	0.01	-	nuc	1					260
P06706 UniProt NPD GO	TNNC_HALRO	Troponin C, body wall muscle	0.01	-	cyt	0					155
P29290 UniProt NPD GO	TNNCA_HOMAM	Troponin C, isoform 2A	0.01	-	cyt	0					150
Q80YP0 UniProt NPD GO	CDK3_MOUSE	Truncated cell division protein kinase 3 homolog	0.01	-	cyt	0					186
P39051 UniProt NPD GO	TYTR_TRYBB	Trypanothione reductase (EC 1.8.1.12) (TR) (N(1),N(8)-bis(glutathionyl)spermidine reductase)	0.01	-	cyt	0	Cytoplasm				492
O77404 UniProt NPD GO	TYPX_TRYBB	Tryparedoxin	0.01	-	mit	0				1O73	144
P29786 UniProt NPD GO	TRY3_AEDAE	Trypsin 3A1 precursor (EC 3.4.21.4)	0.01	-	cyt	0	Secreted protein; extracellular space				254
Q90629 UniProt NPD GO	TRY3_CHICK	Trypsin II-P29 precursor (EC 3.4.21.4)	0.01	-	exc	0	Secreted protein; extracellular space				248
P32821 UniProt NPD GO	TRYA_RAT	Trypsin V-A precursor (EC 3.4.21.4)	0.01	-	exc	0	Secreted protein; extracellular space				246
P35043 UniProt NPD GO	TRYA3_LUCCU	Trypsin alpha-3 (EC 3.4.21.4) (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space				165
P35044 UniProt NPD GO	TRYA4_LUCCU	Trypsin alpha-4 precursor (EC 3.4.21.4)	0.01	-	vac	0	Secreted protein; extracellular space				255
P54627 UniProt NPD GO	TRYE_DROER	Trypsin epsilon precursor (EC 3.4.21.4)	0.01	-	vac	0	Secreted protein; extracellular space				256
P16589 UniProt NPD GO	ITRP_HALRO	Trypsin inhibitor (ATI)	0.01	-	nuc	0	Secreted protein			1IW4	55
P81902 UniProt NPD GO	CSTI_BOMMO	Trypsin inhibitor (Cocoon shell-associated trypsin inhibitor) (CSTI)	0.01	-	nuc	0					55
Q02214 UniProt NPD GO	ITR1_NICSY	Trypsin inhibitor 1 precursor (Trypsin inhibitor I) (NSTI-I)	0.01	-	exc	0	Or: Vacuole (Potential). Or: Secreted protein (Potential)				94
P25700 UniProt NPD GO	IT2_PSOTE	Trypsin inhibitor 2 (WTI-2)	0.01	-	cyt	0					182
P83394 UniProt NPD GO	ITR3_CYCPE	Trypsin inhibitor 3 (Trypsin inhibitor III) (CyPTI-III) [Contains: Trypsin inhibitor 1 (Trypsin inhi ...	0.01	-	nuc	0	Secreted protein				29
P35628 UniProt NPD GO	ITR4_LUFCY	Trypsin inhibitor 4 (Trypsin inhibitor I) (TGTI-I)	0.01	-	nuc	0	Secreted protein				28
P83397 UniProt NPD GO	ITR6_CYCPE	Trypsin inhibitor 6 (Trypsin inhibitor VI) (CyPTI-VI)	0.01	-	nuc	0	Secreted protein				30
P24925 UniProt NPD GO	ITRA_ALBJU	Trypsin inhibitor A chain (Fragment)	0.01	-		0					20
P01070 UniProt NPD GO	ITRA_SOYBN	Trypsin inhibitor A precursor (Kunitz-type trypsin inhibitor A)	0.01	-	end	1 *				1BA7	216
P68170 UniProt NPD GO	IDE3_ERYCO	Trypsin inhibitor DE-3 (Fragment)	0.01	-		0					20
P52905 UniProt NPD GO	TRYI_DROME	Trypsin iota precursor (EC 3.4.21.4)	0.01	-	nuc	0	Secreted protein; extracellular space				252
P00764 UniProt NPD GO	TRYP_SQUAC	Trypsin precursor (EC 3.4.21.4)	0.01	-	cyt	0	Secreted protein; extracellular space				229
P54628 UniProt NPD GO	TRYT_DROER	Trypsin theta precursor (EC 3.4.21.4)	0.01	-	exc	1 *	Secreted protein; extracellular space				262
P16049 UniProt NPD GO	TRY1_GADMO	Trypsin-1 precursor (EC 3.4.21.4) (Trypsin I)	0.01	-	exc	0	Secreted protein; extracellular space				241
P07477 UniProt NPD GO	TRY1_HUMAN	Trypsin-1 precursor (EC 3.4.21.4) (Trypsin I) (Cationic trypsinogen)	0.01	-	exc	0	Secreted protein; extracellular space	extracellular region [NAS]	167800	1TRN	247
Q91041 UniProt NPD GO	TRYX_GADMO	Trypsin-10 precursor (EC 3.4.21.4) (Trypsin X)	0.01	-	exc	0	Secreted protein; extracellular space				241
P83455 UniProt NPD GO	TPFY_PACDA	Tryptophyllin-1 (PdT-1)	0.01	-		0	Secreted protein	extracellular region [NAS]			7
P33626 UniProt NPD GO	TBA4_MAIZE	Tubulin alpha-4 chain (Alpha-4 tubulin) (Fragments)	0.01	-	cyt	0					61
P41273 UniProt NPD GO	TNFL9_HUMAN	Tumor necrosis factor ligand superfamily member 9 (4-1BB ligand) (4-1BBL)	0.01	-	cyt	1 *	Membrane; single-pass type II membrane protein		606182		254
O35734 UniProt NPD GO	TNFA_MARMO	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.01	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P36939 UniProt NPD GO	TNFA_PERLE	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.01	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				235

You are viewing entries 91851 to 91900 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.