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
P49142 UniProt NPD GO	TTHY_PETBR	Transthyretin precursor (Prealbumin)	0.00	-	exc	0	Secreted protein				149
P49143 UniProt NPD GO	TTHY_SMIMA	Transthyretin precursor (Prealbumin)	0.00	-	exc	0	Secreted protein				149
P27731 UniProt NPD GO	TTHY_CHICK	Transthyretin precursor (Prealbumin) (TBPA)	0.00	-	exc	1 *	Secreted protein			1TFP	150
P02767 UniProt NPD GO	TTHY_RAT	Transthyretin precursor (Prealbumin) (TBPA)	0.00	-	exc	0	Secreted protein	extracellular space [IDA]		1RVS	147
Q863B4 UniProt NPD GO	TFF3_CANFA	Trefoil factor 3 precursor (Intestinal trefoil factor)	0.00	-	exc	1 *	Secreted protein (By similarity)				80
Q62395 UniProt NPD GO	TFF3_MOUSE	Trefoil factor 3 precursor (Intestinal trefoil factor)	0.00	-	exc	1 *	Secreted protein	secretory granule [IDA]			81
Q07654 UniProt NPD GO	TFF3_HUMAN	Trefoil factor 3 precursor (Intestinal trefoil factor) (hP1.B)	0.00	-	exc	0	Secreted protein	extracellular region [TAS]	600633	1PE3	80
P01371 UniProt NPD GO	TA10_TREME	Tremerogen A-10	0.00	-		0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				12
Q27172 UniProt NPD GO	T1F_PARTE	Trichocyst matrix protein T1-F (Secretory granule protein T1-F) (TMP 1-F) (Fragment)	0.00	-	cyt	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				33
Q5E956 UniProt NPD GO	TPIS_BOVIN	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.00	-	cyt	0					248
Q29371 UniProt NPD GO	TPIS_PIG	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.00	-	cyt	0					247
Q9GTX8 UniProt NPD GO	TPIS_TAESO	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.00	-	cyt	0	Cytoplasm (Probable)				250
P21820 UniProt NPD GO	TPIS_COPJA	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.00	-	cyt	0	Cytoplasm (Probable)				253
P48495 UniProt NPD GO	TPIS_PETHY	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.00	-	cyt	0	Cytoplasm (Probable)				254
P50162 UniProt NPD GO	TRN1_DATST	Tropinone reductase 1 (EC 1.1.1.206) (Tropinone reductase-I) (TR-I) (Tropine dehydrogenase)	0.00	-	cyt	1				1AE1	273
P47947 UniProt NPD GO	TNNC1_DROME	Troponin C, isoform 1	0.00	-	cyt	0					154
P21798 UniProt NPD GO	TNNC2_BALNU	Troponin C, isoform 2	0.00	-	cyt	0					151
P81074 UniProt NPD GO	TNNC2_PRODO	Troponin C, skeletal muscle (Fragment)	0.00	-	cyt	0					52
P35050 UniProt NPD GO	TRYP_PENMO	Trypsin (EC 3.4.21.4) (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				32
P01074 UniProt NPD GO	ITR1_CUCMA	Trypsin inhibitor 1 (Trypsin inhibitor I) (CMTI-I) (ITD-I)	0.00	-	nuc	0	Secreted protein			3CTI	29
Q43667 UniProt NPD GO	ITR1_TRIKI	Trypsin inhibitor 1 precursor (Trypsin inhibitor I) (TTII)	0.00	-	cyt	0	Secreted protein (By similarity)				65
P81365 UniProt NPD GO	IT1B_ERYVA	Trypsin inhibitor 1B (ETIB)	0.00	-	cyt	0					176
P26780 UniProt NPD GO	ITI2_SINAL	Trypsin inhibitor 2 precursor (MTI-2)	0.00	-	exc	1 *	Secreted protein				99
P10291 UniProt NPD GO	ITR2B_CUCSA	Trypsin inhibitor 2b (Trypsin inhibitor IIB) (CSTI-IIB)	0.00	-	nuc	0	Secreted protein				32
P10293 UniProt NPD GO	ITR3_CUCPE	Trypsin inhibitor 3 (Trypsin inhibitor III) (CPTI-III) [Contains: Trypsin inhibitor 2 (Trypsin inhib ...	0.00	-	nuc	0	Secreted protein			2STB	32
P07853 UniProt NPD GO	ITR4_CUCMA	Trypsin inhibitor 4 (Trypsin inhibitor IV) (CMTI-IV) [Contains: Trypsin inhibitor 3 (Trypsin inhibit ...	0.00	-	nuc	0	Secreted protein				32
P10292 UniProt NPD GO	ITR4_CUCSA	Trypsin inhibitor 4 (Trypsin inhibitor IV) (CSTI-IV)	0.00	-	nuc	0	Secreted protein				30
P84890 UniProt NPD GO	ITRY_ARCEL	Trypsin inhibitor AeTI (Fragment)	0.00	-		0					20
P01071 UniProt NPD GO	ITRB_SOYBN	Trypsin inhibitor B (Kunitz-type trypsin inhibitor B)	0.00	-	cyt	0					181
P24927 UniProt NPD GO	ITRB_ALBJU	Trypsin inhibitor B chain (Fragment)	0.00	-		0					15
P35034 UniProt NPD GO	TRYP_PLEPL	Trypsin precursor (EC 3.4.21.4)	0.00	-	exc	0	Secreted protein; extracellular space				250
P51588 UniProt NPD GO	TRYP_SARBU	Trypsin precursor (EC 3.4.21.4)	0.00	-	mit	0	Secreted protein; extracellular space				254
P81071 UniProt NPD GO	TRYP_FELCA	Trypsin precursor (EC 3.4.21.4) (Fragment)	0.00	-		0	Secreted protein; extracellular space				16
P35051 UniProt NPD GO	TRYP_PROAT	Trypsin precursor (EC 3.4.21.4) (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				21
P35048 UniProt NPD GO	TRYP_SIMVI	Trypsin precursor (EC 3.4.21.4) (Fragment)	0.00	-	end	1 *	Secreted protein; extracellular space				247
P42280 UniProt NPD GO	TRYZ_DROME	Trypsin zeta precursor (EC 3.4.21.4)	0.00	-	exc	1 *	Secreted protein; extracellular space				280
P00765 UniProt NPD GO	TRYP_ASTFL	Trypsin-1 (EC 3.4.21.4) (Trypsin I)	0.00	-	cyt	0	Secreted protein; extracellular space				237
P35031 UniProt NPD GO	TRY1_SALSA	Trypsin-1 precursor (EC 3.4.21.4) (Trypsin I)	0.00	-	vac	0	Secreted protein; extracellular space			2TBS	242
P07478 UniProt NPD GO	TRY2_HUMAN	Trypsin-2 precursor (EC 3.4.21.4) (Trypsin II) (Anionic trypsinogen)	0.00	-	exc	0	Secreted protein; extracellular space	extracellular matrix [TAS] extracellular region [IDA] extracellular space [IMP]	601564		247
P35032 UniProt NPD GO	TRY2_SALSA	Trypsin-2 precursor (EC 3.4.21.4) (Trypsin II) (Fragment)	0.00	-	nuc	0	Secreted protein; extracellular space				231
P35030 UniProt NPD GO	TRY3_HUMAN	Trypsin-3 precursor (EC 3.4.21.4) (Trypsin III) (Brain trypsinogen) (Mesotrypsinogen) (Trypsin IV)	0.00	-	cyt	0	Secreted protein	extracellular space [IDA]		1H4W	304
O22018 UniProt NPD GO	TRPA_CYAME	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.00	-	cyt	0	Plastid; chloroplast				243
P84215 UniProt NPD GO	TY13_BOMVA	Tryptophyllin-13	0.00	-		0	Secreted protein	extracellular region [IDA]			14
P84833 UniProt NPD GO	TY3_ASCTR	Tryptophyllin-3	0.00	-		0	Secreted protein	extracellular region [IDA]			6
Q08628 UniProt NPD GO	TBA_BLEJA	Tubulin alpha chain (Fragment)	0.00	-	cyt	0					50
P33628 UniProt NPD GO	TBA_PICAB	Tubulin alpha chain (Fragment)	0.00	-	cyt	0					113
P84549 UniProt NPD GO	TBA_POPEU	Tubulin alpha chain (Fragments)	0.00	-	cyt	0					50
P81947 UniProt NPD GO	TBAK_BOVIN	Tubulin alpha-ubiquitous chain (Alpha-tubulin ubiquitous) (Tubulin K-alpha-1) (Fragment)	0.00	-	cyt	0					22
O42449 UniProt NPD GO	IOD1_ORENI	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.00	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				248
Q6RW13 UniProt NPD GO	ATRAP_HUMAN	Type-1 angiotensin II receptor-associated protein (AT1 receptor-associated protein)	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...		608729		159

You are viewing entries 98401 to 98450 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.