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
Q9WVM6 UniProt NPD GO	TLL2_MOUSE	Tolloid-like protein 2 precursor (EC 3.4.24.-)	0.20	-	vac	0	Secreted protein (Probable)				1012
P01413 UniProt NPD GO	TX51_DENJA	Toxin S5C1	0.20	-	nuc	0	Secreted protein				61
P13781 UniProt NPD GO	REP2_ZYGBI	Trans-acting factor C (REP2)	0.20	-	cyt	0					178
Q9TVQ5 UniProt NPD GO	SPT4H_DROME	Transcription elongation factor SPT4 (dSpt4) (DRB sensitivity-inducing factor small subunit) (DSIF s ...	0.20	-	nuc	0	Nucleus (By similarity)	nucleus [ISS] polytene chromosome interband [IDA] polytene chromosome puff [IDA]			116
Q9IA78 UniProt NPD GO	T2AG_PAROL	Transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TFIIA-gamma ...	0.20	-	mit	0	Nucleus				111
Q08873 UniProt NPD GO	SCP1_YEAST	Transgelin (Calponin homolog 1)	0.20	-	nuc	0	Actin patch. Cortical actin patches	actin cortical patch [IDA]			200
Q95GN8 UniProt NPD GO	IF1C_CABCA	Translation initiation factor IF-1, chloroplast	0.20	-	cyt	0	Plastid; chloroplast				77
Q6EW17 UniProt NPD GO	IF1C_NYMAL	Translation initiation factor IF-1, chloroplast	0.20	-	cyt	0	Plastid; chloroplast				77
Q91YJ5 UniProt NPD GO	IF2M_MOUSE	Translation initiation factor IF-2, mitochondrial precursor (IF-2Mt) (IF-2(Mt))	0.20	+	nuc	0	Mitochondrion (By similarity)			2CRV	727
Q969X1 UniProt NPD GO	TMBI1_HUMAN	Transmembrane BAX inhibitor motif-containing protein 1 (RECS1 protein homolog)	0.20	-	end	7	Membrane; multi-pass membrane protein (By similarity)				311
Q3ZBI9 UniProt NPD GO	TMUB1_BOVIN	Transmembrane and ubiquitin-like domain-containing protein 1	0.20	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				246
Q8IU80 UniProt NPD GO	TMPS6_HUMAN	Transmembrane protease, serine 6 (EC 3.4.21.-) (Matriptase-2)	0.20	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to membrane [IDA]	609862		802
Q80VP8 UniProt NPD GO	T106C_MOUSE	Transmembrane protein 106C	0.20	-	gol	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				260
Q8N4L2 UniProt NPD GO	TM55A_HUMAN	Transmembrane protein 55A (EC 3.1.3.-) (Type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.20	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein. Lysosome; lysosomal m ...		609864		257
Q86T03 UniProt NPD GO	TM55B_HUMAN	Transmembrane protein 55B (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.20	-	mit	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein. Lysosome; lysosomal m ...		609865		277
Q9HCN3 UniProt NPD GO	TMEM8_HUMAN	Transmembrane protein 8 precursor (M83 protein)	0.20	-	end	4	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [NAS]			771
Q9P7N9 UniProt NPD GO	TRS31_SCHPO	Transport protein particle subunit trs31 (TRAPP subunit trs31)	0.20	-	nuc	0					209
Q9LVM5 UniProt NPD GO	TTHL_ARATH	Transthyretin-like protein	0.20	-	nuc	0	Cell membrane; peripheral membrane protein				324
Q863J2 UniProt NPD GO	TFF2_CANFA	Trefoil factor 2 precursor	0.20	-	exc	0	Secreted protein (By similarity)				129
P27679 UniProt NPD GO	TRI5_GIBPU	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.20	-	cyt	0					383
Q9UGM6 UniProt NPD GO	SYWM_HUMAN	Tryptophanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS) ...	0.20	-	nuc	0	Mitochondrion; mitochondrial matrix		604733		360
P04691 UniProt NPD GO	TBB1_RAT	Tubulin beta chain (T beta-15)	0.20	-	cyt	0					445
P22013 UniProt NPD GO	TBB1_COLGR	Tubulin beta-1 chain (Beta-1 tubulin)	0.20	-	cyt	0					445
Q9ZRB1 UniProt NPD GO	TBB2_WHEAT	Tubulin beta-2 chain (Beta-2 tubulin)	0.20	-	cyt	0					447
Q94571 UniProt NPD GO	TBB2_HOMAM	Tubulin beta-2 chain (Beta-II tubulin)	0.20	-	cyt	0					452
P09652 UniProt NPD GO	TBB4_CHICK	Tubulin beta-4 chain (Beta-tubulin class-III)	0.20	-	cyt	0					449
Q8HZV4 UniProt NPD GO	TBD_CANFA	Tubulin delta chain (Delta tubulin)	0.20	-	cyt	0	Centrosome (By similarity). Associated with centrioles. Cytoplasm (By similarity). Nucleus (By simil ...				453
Q9R1K7 UniProt NPD GO	TBD_MOUSE	Tubulin delta chain (Delta tubulin)	0.20	-	cyt	0	Centrosome. Associated with centrioles. Cytoplasm. Nucleus. Both cytoplasmic and nuclear	cytoplasm [IDA] nucleus [IDA]			455
P34786 UniProt NPD GO	TBG1_EUPOC	Tubulin gamma-1 chain (Gamma-1 tubulin)	0.20	-	cyt	0					461
Q99JR5 UniProt NPD GO	TINAL_MOUSE	Tubulointerstitial nephritis antigen-like precursor (Androgen-regulated gene 1 protein) (Adrenocorti ...	0.20	+	vac	0	Secreted protein				466
Q9Z0W1 UniProt NPD GO	TNR16_MOUSE	Tumor necrosis factor receptor superfamily member 16 precursor (Low-affinity nerve growth factor rec ...	0.20	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				417
Q9N092 UniProt NPD GO	TR19L_MACFA	Tumor necrosis factor receptor superfamily member 19L precursor (Receptor expressed in lymphoid tiss ...	0.20	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				430
P20334 UniProt NPD GO	TNR9_MOUSE	Tumor necrosis factor receptor superfamily member 9 precursor (4-1BB ligand receptor) (T-cell antige ...	0.20	-	exc	1	Membrane; single-pass type I membrane protein			1D0J	256
Q62393 UniProt NPD GO	TPD52_MOUSE	Tumor protein D52 (mD52)	0.20	-	nuc	0		cytoplasm [ISS] endoplasmic reticulum [ISS] perinuclear region [ISS]			185
Q9ZWS9 UniProt NPD GO	ARR3_ARATH	Two-component response regulator ARR3	0.20	-	nuc	0	Nucleus (Probable)				231
O42412 UniProt NPD GO	IOD3_CHICK	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.20	-	mit	0	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				258
P49899 UniProt NPD GO	IOD3_XENLA	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.20	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				271
Q56TU0 UniProt NPD GO	AFP4_GADMO	Type-4 ice-structuring protein precursor (Antifreeze protein type IV)	0.20	-	exc	0	Secreted protein (By similarity)				125
P55033 UniProt NPD GO	TYRO_FELCA	Tyrosinase (EC 1.14.18.1) (Monophenol monooxygenase) (Fragment)	0.20	-	nuc	0	Melanosome; melanosomal membrane; single-pass type I membrane protein				80
P42688 UniProt NPD GO	SRK2_SPOLA	Tyrosine-protein kinase SRK2 (EC 2.7.10.2) (Fragment)	0.20	-	cyt	0	Cytoplasm (Probable)				362
Q9BV90 UniProt NPD GO	CP033_HUMAN	U11/U12 snRNP 25 kDa protein (Minus-99 protein)	0.20	-	cyt	0	Nucleus	minor (U12-dependent) spliceosome complex [IDA]			132
Q9BUW7 UniProt NPD GO	CI016_HUMAN	UPF0184 protein C9orf16 (EST00098)	0.20	-	nuc	0					83
Q9UTL0 UniProt NPD GO	YIVG_SCHPO	UPF0195 protein C144.16	0.20	-	nuc	0					179
Q9P7D6 UniProt NPD GO	YOFC_SCHPO	UPF0303 protein P4H10.12	0.20	-	cyt	1					171
Q7L5D6 UniProt NPD GO	CG020_HUMAN	UPF0363 protein C7orf20	0.20	-	nuc	0					327
P49729 UniProt NPD GO	UCRI1_TOBAC	Ubiquinol-cytochrome c reductase iron-sulfur subunit 1, mitochondrial precursor (EC 1.10.2.2) (Riesk ...	0.20	-	mit	1	Mitochondrion; mitochondrial inner membrane				258
Q66L51 UniProt NPD GO	COQ5_BRARE	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.20	-	mit	0	Mitochondrion (By similarity)				327
P34666 UniProt NPD GO	COQ5_CAEEL	Ubiquinone biosynthesis methyltransferase coq-5, mitochondrial precursor (EC 2.1.1.-)	0.20	-	mit	0	Mitochondrion (By similarity)				285
P49634 UniProt NPD GO	UBIQ_ACACA	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P42740 UniProt NPD GO	UBIQ_AGLNE	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76

You are viewing entries 51301 to 51350 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.