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
Q64159 UniProt NPD GO	CD3G_RAT	T-cell surface glycoprotein CD3 gamma chain precursor (T-cell receptor T3 gamma chain)	0.33	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] T cell receptor complex [ISS]			182
P33681 UniProt NPD GO	CD80_HUMAN	T-lymphocyte activation antigen CD80 precursor (Activation B7-1 antigen) (CTLA-4 counter-receptor B7 ...	0.33	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [IC] plasma membrane [NAS]	112203	1I8L	288
P26342 UniProt NPD GO	TGBR3_RAT	TGF-beta receptor type III precursor (TGFR-3) (Transforming growth factor beta receptor III) (Betagl ...	0.33	-	exc	1	Cell membrane; single-pass type I membrane protein. Secreted protein; serum. Secreted protein; extra ...				853
Q5R8H1 UniProt NPD GO	TPSNR_PONPY	Tapasin-related protein precursor (TAPASIN-R) (Tapasin-like) (TAP-binding protein-related protein) ( ...	0.33	-	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Endoplasmic reticulum; endoplasm ...				468
Q645U2 UniProt NPD GO	TA2R3_PONPY	Taste receptor type 2 member 3 (T2R3)	0.33	-	end	7 *	Membrane; multi-pass membrane protein				315
Q8BZ64 UniProt NPD GO	TECT1_MOUSE	Tectonic-1 precursor	0.33	-	nuc	0	Secreted protein				593
Q9UQP3 UniProt NPD GO	TENN_HUMAN	Tenascin-N precursor (TN-N)	0.33	-	vac	0					1299
Q9M7D0 UniProt NPD GO	TPSD9_ABIGR	Terpinolene synthase, chloroplast precursor (EC 4.2.3.-) (Aggteo)	0.33	-	cyt	0	Plastid; chloroplast (By similarity)				630
Q96BS2 UniProt NPD GO	TESC_HUMAN	Tescalcin (TSC)	0.33	-	cyt	0		cytoplasm [ISS] lamellipodium [ISS] nucleus [ISS] ruffle [ISS]			214
Q8NBP0 UniProt NPD GO	TTC13_HUMAN	Tetratricopeptide repeat protein 13 (TPR repeat protein 13)	0.33	-	mit	1 *					859
Q99LG4 UniProt NPD GO	TTC5_MOUSE	Tetratricopeptide repeat protein 5 (TPR repeat protein 5)	0.33	-	nuc	0					440
Q715S9 UniProt NPD GO	TXND3_RAT	Thioredoxin domain-containing protein 3 (Spermatid-specific thioredoxin-2) (Sptrx-2)	0.33	-	cyt	0	Cytoplasm. In spermatozoa, it is an integral component of the FS				587
Q8K581 UniProt NPD GO	TXND9_RAT	Thioredoxin domain-containing protein 9 (ES cell-related protein)	0.33	-	cyt	0					226
Q9BQ50 UniProt NPD GO	TREX2_HUMAN	Three prime repair exonuclease 2 (EC 3.1.11.2) (3'-5' exonuclease TREX2)	0.33	-	nuc	0	Nucleus (Probable)		300370	1Y97	279
Q5XHY5 UniProt NPD GO	SYTC_RAT	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.33	-	cyt	0	Cytoplasm				695
Q95116 UniProt NPD GO	TSP2_BOVIN	Thrombospondin-2 precursor (Corticotropin-induced secreted protein) (CISP)	0.33	-	exc	0					1170
Q96HR3 UniProt NPD GO	TR25_HUMAN	Thyroid hormone receptor-associated protein 6 (Thyroid hormone receptor-associated protein complex 2 ...	0.33	-	nuc	0	Nucleus (Potential)	mediator complex [IDA] nucleus [IDA]			178
Q6PGF3 UniProt NPD GO	TR95_MOUSE	Thyroid hormone receptor-associated protein complex 95 kDa component (Trap95) (Thyroid hormone recep ...	0.33	-	cyt	0	Nucleus	mediator complex [ISS] nucleus [ISS]			828
O60602 UniProt NPD GO	TLR5_HUMAN	Toll-like receptor 5 precursor (Toll/interleukin-1 receptor-like protein 3)	0.33	-	vac	1 *	Membrane; single-pass type I membrane protein (By similarity)		603031	1P95	858
O43897 UniProt NPD GO	TLL1_HUMAN	Tolloid-like protein 1 precursor (EC 3.4.24.-)	0.33	-	cyt	0	Secreted protein (Probable)		606742		1013
Q9DER7 UniProt NPD GO	TLL1_CHICK	Tolloid-like protein 1 precursor (EC 3.4.24.-) (Chicken tolloid-like protein 1) (Metalloprotease col ...	0.33	-	exc	0	Secreted protein				1008
Q8JI28 UniProt NPD GO	TLL1_XENLA	Tolloid-like protein 1 precursor (EC 3.4.24.-) (Xenopus tolloid-like protein 1) (Metalloprotease xol ...	0.33	-	exc	0	Secreted protein (By similarity)				1007
Q9BQ92 UniProt NPD GO	TTY7_HUMAN	Transcript Y 7 protein (Fragment)	0.33	-	nuc	0					124
Q60756 UniProt NPD GO	TCF15_MOUSE	Transcription factor 15 (bHLH-EC2 protein) (Paraxis) (Meso1)	0.33	-	nuc	0	Nucleus (By similarity)				195
Q8K4J2 UniProt NPD GO	COE4_MOUSE	Transcription factor COE4 (Early B-cell factor 4) (EBF-4) (Olf-1/EBF-like 4) (OE-4) (O/E-4)	0.33	-	nuc	0	Nucleus (Potential)				599
Q5E9F5 UniProt NPD GO	TAGL2_BOVIN	Transgelin-2	0.33	-	nuc	0					198
Q6RX08 UniProt NPD GO	TRPV1_RABIT	Transient receptor potential cation channel subfamily V member 1 (TrpV1) (osm-9-like TRP channel 1) ...	0.33	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				842
Q8NER1 UniProt NPD GO	TRPV1_HUMAN	Transient receptor potential cation channel subfamily V member 1 (TrpV1) (osm-9-like TRP channel 1) ...	0.33	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)		602076		839
Q9JIP0 UniProt NPD GO	TRPV5_RAT	Transient receptor potential cation channel subfamily V member 5 (TrpV5) (osm-9-like TRP channel 3) ...	0.33	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein. Colocalized with S100A10 and ANAX2 ...	integral to plasma membrane [ISS]			723
Q85FI8 UniProt NPD GO	IF1C_ADICA	Translation initiation factor IF-1, chloroplast	0.33	-	nuc	0	Plastid; chloroplast				80
Q6END9 UniProt NPD GO	IF1C_ORYNI	Translation initiation factor IF-1, chloroplast	0.33	-	nuc	0	Plastid; chloroplast				107
P12135 UniProt NPD GO	IF1C_ORYSA	Translation initiation factor IF-1, chloroplast	0.33	-	nuc	0	Plastid; chloroplast				107
P46199 UniProt NPD GO	IF2M_HUMAN	Translation initiation factor IF-2, mitochondrial precursor (IF-2Mt) (IF-2(Mt))	0.33	-	mit	0	Mitochondrion	mitochondrion [TAS]	603766		727
Q64350 UniProt NPD GO	EI2BE_RAT	Translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subunit epsilon ...	0.33	-	cyt	0		eukaryotic translation initiation factor 2B... [TAS]			716
Q6UXZ0 UniProt NPD GO	TMIGD_HUMAN	Transmembrane and immunoglobulin domain-containing protein precursor	0.33	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				262
Q9CQG0 UniProt NPD GO	TMED6_MOUSE	Transmembrane emp24 domain-containing protein 6 precursor	0.33	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				239
Q9CR67 UniProt NPD GO	TMM33_MOUSE	Transmembrane protein 33 (DB83 protein)	0.33	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				247
Q9BXS4 UniProt NPD GO	TMM59_HUMAN	Transmembrane protein 59 precursor (Liver membrane-bound protein)	0.33	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				323
Q9QY73 UniProt NPD GO	TMM59_MOUSE	Transmembrane protein 59 precursor (Thymic dendritic cell-derived factor 1)	0.33	-	end	1	Membrane; single-pass type I membrane protein (Potential)				323
Q03784 UniProt NPD GO	TRS23_YEAST	Transport protein particle 23 kDa subunit (TRAPP 23 kDa subunit)	0.33	-	nuc	0		TRAPP complex [IDA]			219
Q5GLH2 UniProt NPD GO	TRIB2_BOVIN	Tribbles homolog 2 (TRB-2)	0.33	-	mit	0	Cytoplasm (By similarity). May associate with the cytoskeleton (By similarity)	cytoplasm [ISS]			343
Q28283 UniProt NPD GO	TRIB2_CANFA	Tribbles homolog 2 (TRB-2)	0.33	-	mit	0	Cytoplasm. May associate with the cytoskeleton	cytoplasm [IDA]			343
Q5R669 UniProt NPD GO	TRIB2_PONPY	Tribbles homolog 2 (TRB-2)	0.33	-	mit	0	Cytoplasm (By similarity). May associate with the cytoskeleton (By similarity)	cytoplasm [ISS]			343
Q27182 UniProt NPD GO	T4A_PARTE	Trichocyst matrix protein T4-A precursor (Secretory granule protein T4-A) (TMP 4-A) [Contains: Trich ...	0.33	-	exc	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				363
O70277 UniProt NPD GO	TRIM3_RAT	Tripartite motif-containing protein 3 (RING finger protein 22) (Brain-expressed RING finger protein) ...	0.33	-	cyt	0	Cytoplasm (By similarity)				744
Q02088 UniProt NPD GO	TPM_SCHPO	Tropomyosin	0.33	-	nuc	0		actin cable [IDA]			161
O96764 UniProt NPD GO	TPM_CHIKI	Tropomyosin (Allergen Chi k 10)	0.33	-	nuc	0					285
P40414 UniProt NPD GO	TPM2_YEAST	Tropomyosin 2	0.33	-	nuc	0		actin cable [IDA] contractile ring (sensu Saccharomyces) [IDA]			161
P19352 UniProt NPD GO	TPM2_CHICK	Tropomyosin beta chain (Tropomyosin 2) (Beta-tropomyosin)	0.33	-	nuc	0					284
Q5EBG2 UniProt NPD GO	T23O_XENTR	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.33	-	cyt	0					406

You are viewing entries 38051 to 38100 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.