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
P14214 UniProt NPD GO	TAC2_TACTR	Tachyplesin-2 precursor (Tachyplesin II)	0.12	-	cyt	0	Secreted protein. S-granules				77
Q9BY14 UniProt NPD GO	TX101_HUMAN	Testis-expressed protein 101 precursor (Scleroderma-associated autoantigen) (Cell surface receptor N ...	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor Associated with lipid rafts (By similarity)				249
P05452 UniProt NPD GO	TETN_HUMAN	Tetranectin precursor (TN) (C-type lectin domain family 3 member B) (Plasminogen kringle 4-binding p ...	0.12	-	mit	0	Secreted protein	extracellular region [NAS]	187520	1TN3	202
P02884 UniProt NPD GO	THM2_THADA	Thaumatin-2 precursor (Thaumatin II)	0.12	-	exc	1 *	Cytoplasmic vesicle. Thaumatin accumulates in vesicle-like organelles				235
P83746 UniProt NPD GO	TX2_THEBL	Theraphotoxin-2 (TlTx2)	0.12	-	nuc	0	Secreted protein				35
Q99PL8 UniProt NPD GO	S19A3_MOUSE	Thiamine transporter 2 (ThTr-2) (ThTr2) (Solute carrier family 19 member 3)	0.12	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				488
Q9XFH8 UniProt NPD GO	TRXF1_ARATH	Thioredoxin F-type 1, chloroplast precursor (TRX-F1)	0.12	-	mit	0	Plastid; chloroplast (By similarity)				178
O22160 UniProt NPD GO	TL15_ARATH	Thylakoid lumenal 15 kDa protein, chloroplast precursor (p15)	0.12	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen	thylakoid lumen (sensu Viridiplantae) [IDA]			224
P63314 UniProt NPD GO	TYB10_HORSE	Thymosin beta-10	0.12	-	nuc	0	Cytoplasm				43
P63313 UniProt NPD GO	TYB10_HUMAN	Thymosin beta-10	0.12	-	nuc	0	Cytoplasm		188399		43
Q6ZWY8 UniProt NPD GO	TYB10_MOUSE	Thymosin beta-10	0.12	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IC]			43
P63312 UniProt NPD GO	TYB10_RAT	Thymosin beta-10	0.12	-	nuc	0	Cytoplasm				43
P18758 UniProt NPD GO	TYB4_XENLA	Thymosin beta-4 (T beta 4) (Thymosin beta 4Xen)	0.12	-	nuc	0	Cytoplasm				43
Q7YRC3 UniProt NPD GO	TYB4_MACEU	Thymosin beta-4 (T beta 4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.12	-	nuc	0	Cytoplasm (By similarity)				43
O14604 UniProt NPD GO	TYB4Y_HUMAN	Thymosin beta-4, Y-chromosomal	0.12	-	nuc	0	Cytoplasm (By similarity)		400017		43
Q9I954 UniProt NPD GO	TYBB_CYPCA	Thymosin beta-b	0.12	-	nuc	0	Cytoplasm (By similarity)				42
P34079 UniProt NPD GO	TXPL2_PLETR	Toxin PLTX-2 (PLTX-II)	0.12	-	nuc	0	Secreted protein				44
Q9P1P5 UniProt NPD GO	TAAR2_HUMAN	Trace amine-associated receptor 2 (G-protein coupled receptor 58)	0.12	-	end	7 *	Membrane; multi-pass membrane protein		604849		351
Q78XR0 UniProt NPD GO	TPC6A_MOUSE	Trafficking protein particle complex subunit 6A	0.12	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				159
Q9BV79 UniProt NPD GO	MECR_HUMAN	Trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38) (HsNrbf-1) (NRBF-1)	0.12	-	mit	0	Mitochondrion	mitochondrion [IDA]	608205	1ZSY	373
Q43033 UniProt NPD GO	TCMO_PETCR	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.12	-	end	1 *					506
Q93092 UniProt NPD GO	TALDO_MOUSE	Transaldolase (EC 2.2.1.2)	0.12	-	mit	0	Cytoplasm (Probable)			2CWN	337
Q4WU00 UniProt NPD GO	SPT4_ASPFU	Transcription elongation factor spt4 (Chromatin elongation factor spt4)	0.12	-	mit	0	Nucleus. Centromere and heterochromatin (By similarity)				156
O94039 UniProt NPD GO	TKT1_CANAL	Transketolase 1 (EC 2.2.1.1) (TK 1)	0.12	-	cyt	0					677
Q5RE32 UniProt NPD GO	TMEDA_PONPY	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (21 kDa tra ...	0.12	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side (By similarity)				219
Q63584 UniProt NPD GO	TMEDA_RAT	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (21 kDa tra ...	0.12	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side (By similarity)	integral to membrane [IDA] microsome [IDA] zymogen granule membrane [IDA]			219
Q78IS1 UniProt NPD GO	TMED3_MOUSE	Transmembrane emp24 domain-containing protein 3 precursor	0.12	-	nuc	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				221
Q8VHK8 UniProt NPD GO	TM11D_MOUSE	Transmembrane protease, serine 11D precursor (EC 3.4.21.-) (Airway trypsin-like protease) (AT) (Adre ...	0.12	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				417
Q12612 UniProt NPD GO	TRI4_FUSSP	Trichodiene oxygenase (EC 1.14.-.-) (Cytochrome P450 58)	0.12	-	nuc	1 *					520
Q8NID7 UniProt NPD GO	TRI5_FUSPS	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.12	-	cyt	0					375
Q8JI39 UniProt NPD GO	CRVP_TRIFL	Triflin precursor	0.12	-	exc	0	Secreted protein			1WVR	240
Q64428 UniProt NPD GO	ECHA_RAT	Trifunctional enzyme subunit alpha, mitochondrial precursor (TP-alpha) [Includes: Long-chain enoyl-C ...	0.12	-	mit	0	Mitochondrion; mitochondrial matrix	fatty acid beta-oxidation multienzyme complex [TAS] mitochondrion [TAS]			763
Q64737 UniProt NPD GO	PUR2_MOUSE	Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase ...	0.12	-	cyt	0					1010
Q8SAS8 UniProt NPD GO	TBSYN_HYPAN	Trihydroxybenzophenone synthase (EC 2.3.1.-)	0.12	-	cyt	0					395
P35033 UniProt NPD GO	TRY3_SALSA	Trypsin-3 precursor (EC 3.4.21.4) (Trypsin III) (Fragment)	0.12	-	nuc	0	Secreted protein; extracellular space			1A0J	238
P15157 UniProt NPD GO	TRYA1_HUMAN	Tryptase alpha-1 precursor (EC 3.4.21.59) (Tryptase-1)	0.12	-	end	0	Released from the secretory granules upon mast cell activation		191080	2F9P	275
P84834 UniProt NPD GO	TY2_ASCTR	Tryptophyllin-2	0.12	-		0	Secreted protein	extracellular region [IDA]			9
Q08114 UniProt NPD GO	TBA_EUPOC	Tubulin alpha chain	0.12	-	cyt	0					450
Q91060 UniProt NPD GO	TBA_NOTVI	Tubulin alpha chain	0.12	-	cyt	0					450
P28287 UniProt NPD GO	TBA_OXYGR	Tubulin alpha chain	0.12	-	cyt	0					450
P02550 UniProt NPD GO	TBA_PIG	Tubulin alpha chain	0.12	-	cyt	0				1TVK	451
P14642 UniProt NPD GO	TBA_PLAFK	Tubulin alpha chain	0.12	-	cyt	0					453
P10872 UniProt NPD GO	TBA_TETPY	Tubulin alpha chain	0.12	-	cyt	0					449
P41351 UniProt NPD GO	TBA_TETTH	Tubulin alpha chain	0.12	-	cyt	0					449
Q8WQ47 UniProt NPD GO	TBA_LEPDS	Tubulin alpha chain (Allergen Lep d ?)	0.12	-	cyt	0					450
Q71G51 UniProt NPD GO	TBA_NEOCA	Tubulin alpha chain (Alpha tubulin)	0.12	-	cyt	0					453
P10873 UniProt NPD GO	TBA_TOXGO	Tubulin alpha chain (Alpha tubulin)	0.12	-	cyt	0					453
P53371 UniProt NPD GO	TBA_AJECA	Tubulin alpha chain (Fragment)	0.12	-	cyt	0					418
Q8T6A5 UniProt NPD GO	TBA1_APLCA	Tubulin alpha-1 chain	0.12	-	cyt	0					451
P18258 UniProt NPD GO	TBA1_PARLI	Tubulin alpha-1 chain	0.12	-	cyt	0					452

You are viewing entries 62001 to 62050 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.