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
Q9TWR5 UniProt NPD GO	TXV2_PHONI	Toxin PnV2 (Fragment)	0.17	-		0	Secreted protein				20
P01419 UniProt NPD GO	TX510_DENJA	Toxin S5C10	0.17	-	nuc	0	Secreted protein				58
P92994 UniProt NPD GO	TCMO_ARATH	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.17	-	end	0					505
Q43067 UniProt NPD GO	TCMO_PEA	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.17	+	end	0					505
Q12962 UniProt NPD GO	TAF10_HUMAN	Transcription initiation factor TFIID subunit 10 (Transcription initiation factor TFIID 30 kDa subun ...	0.17	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	600475		218
P25490 UniProt NPD GO	TYY1_HUMAN	Transcriptional repressor protein YY1 (Yin and yang 1) (YY-1) (Delta transcription factor) (NF-E1)	0.17	+	cyt	0	Nucleus; nucleoplasm; nuclear matrix. Associated with the nuclear matrix		600013	1ZNM	414
Q9JKX3 UniProt NPD GO	TFR2_MOUSE	Transferrin receptor protein 2 (TfR2)	0.17	-	mit	1	Cell membrane; single-pass type II membrane protein. Isoform 3: Cytoplasm				798
Q8R455 UniProt NPD GO	TRPM8_RAT	Transient receptor potential cation channel subfamily M member 8 (Cold menthol receptor 1)	0.17	-	end	7	Membrane; multi-pass membrane protein (Probable)				1104
Q95GM3 UniProt NPD GO	IF1C_BOROF	Translation initiation factor IF-1, chloroplast	0.17	-	cyt	0	Plastid; chloroplast				77
O82499 UniProt NPD GO	IF1C_ARATH	Translation initiation factor IF-1, chloroplast precursor	0.17	-	mit	0	Plastid; chloroplast				141
P84157 UniProt NPD GO	TMAP1_HUMAN	Transmembrane anchor protein 1	0.17	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				204
P49755 UniProt NPD GO	TMEDA_HUMAN	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (21 kDa tra ...	0.17	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side (By similarity)	ER-Golgi intermediate compartment [IDA] integral to plasma membrane [TAS] membrane fraction [TAS] microsome [ISS] plasma membrane [TAS] zymogen granule membrane [ISS]	605406		219
Q9BZD7 UniProt NPD GO	TMG3_HUMAN	Transmembrane gamma-carboxyglutamic acid protein 3 precursor (Proline-rich Gla protein 3) (Proline-r ...	0.17	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			231
Q6PAQ9 UniProt NPD GO	TMG3_MOUSE	Transmembrane gamma-carboxyglutamic acid protein 3 precursor (Proline-rich Gla protein 3) (Proline-r ...	0.17	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				231
Q99P91 UniProt NPD GO	GPNMB_MOUSE	Transmembrane glycoprotein NMB precursor (Dendritic cell-associated transmembrane protein) (DC-HIL)	0.17	-	end	1	Intracytoplasmic membrane; single-pass type I membrane protein. Vesicular, endosomal like structures ...	cytoplasmic membrane-bound vesicle [IDA] integral to plasma membrane [IDA]			574
Q9UL52 UniProt NPD GO	TM11E_HUMAN	Transmembrane protease, serine 11E precursor (EC 3.4.21.-) (Serine protease DESC1) [Contains: Transm ...	0.17	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to plasma membrane [ISS]			423
Q7Z410 UniProt NPD GO	TMPS9_HUMAN	Transmembrane protease, serine 9 (EC 3.4.21.-) (Polyserase-1) (Polyserase-I) (Polyserine protease 1) ...	0.17	-	mit	1 *	Cell membrane; single-pass type II membrane protein				1059
Q5RFN8 UniProt NPD GO	TM101_PONPY	Transmembrane protein 101	0.17	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				257
Q9CZX7 UniProt NPD GO	TM55A_MOUSE	Transmembrane protein 55A (EC 3.1.3.-) (Type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.17	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				257
Q96N35 UniProt NPD GO	TMM83_HUMAN	Transmembrane protein 83	0.17	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				136
Q9CR23 UniProt NPD GO	TMEM9_MOUSE	Transmembrane protein 9 precursor	0.17	-	end	1	Endosome; late endosome; late endosomal membrane; single-pass type I membrane protein (By similarity ...	late endosome [ISS] lysosome [ISS]			183
P38925 UniProt NPD GO	SMF1_YEAST	Transporter protein SMF1/ESP1	0.17	-	end	11	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA] vacuole (sensu Fungi) [IDA]			575
Q6P2B1 UniProt NPD GO	TNPO3_MOUSE	Transportin-3	0.17	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				923
Q8NIH0 UniProt NPD GO	TRI5_FUSAU	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.17	-	cyt	0					375
Q29147 UniProt NPD GO	TRIC_TRIVU	Trichosurin precursor	0.17	-	exc	0	Secreted protein				180
P49133 UniProt NPD GO	TPT_MAIZE	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT)	0.17	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				409
P82410 UniProt NPD GO	ITR3_MOMCO	Trypsin inhibitor 3 (Trypsin inhibitor III) (MCoTI-III)	0.17	-	nuc	0	Secreted protein				30
P01088 UniProt NPD GO	ITRF_MAIZE	Trypsin/factor XIIA inhibitor precursor (Hageman factor inhibitor) (CHFI)	0.17	-	mit	1 *	Secreted protein			1BFA	155
P49742 UniProt NPD GO	TBAB_SCHCO	Tubulin alpha-1B chain	0.17	-	cyt	0					446
Q2U2U3 UniProt NPD GO	TBB_ASPOR	Tubulin beta chain (Beta tubulin)	0.17	-	cyt	0					448
P41385 UniProt NPD GO	TBB_BOMMO	Tubulin beta chain (Beta tubulin)	0.17	-	cyt	0					450
P32256 UniProt NPD GO	TBB_DICDI	Tubulin beta chain (Beta tubulin)	0.17	-	cyt	0					455
P30668 UniProt NPD GO	TBB_SCHCO	Tubulin beta chain (Beta tubulin)	0.17	-	cyt	0					445
P18025 UniProt NPD GO	TBB1_MAIZE	Tubulin beta-1 chain (Beta-1 tubulin)	0.17	-	cyt	0					446
P09203 UniProt NPD GO	TBB1_CHICK	Tubulin beta-1 chain (Beta-tubulin class-I)	0.17	-	cyt	0					445
P29502 UniProt NPD GO	TBB3_PEA	Tubulin beta-3 chain (Beta-3 tubulin) (Fragment)	0.17	-	cyt	0					440
Q9ZRA8 UniProt NPD GO	TBB5_WHEAT	Tubulin beta-5 chain (Beta-5 tubulin)	0.17	-	cyt	0					447
P29514 UniProt NPD GO	TBB6_ARATH	Tubulin beta-6 chain (Beta-6 tubulin)	0.17	-	cyt	0					449
Q9D1E6 UniProt NPD GO	TBCB_MOUSE	Tubulin-specific chaperone B (Tubulin folding cofactor B) (Cytoskeleton-associated protein 1) (Cytos ...	0.17	-	cyt	0				1WHG	244
Q9ER62 UniProt NPD GO	TNR22_MOUSE	Tumor necrosis factor receptor superfamily member 22 (Tumor necrosis factor receptor p60 homolog 2) ...	0.17	-	exc	2 *	Isoform 1: Cell membrane; single-pass type II membrane protein (Potential). Isoform 2: Secreted prot ...	integral to membrane [NAS]			198
P24389 UniProt NPD GO	IOD1_RAT	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.17	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				257
P00440 UniProt NPD GO	TYRO_NEUCR	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.17	-	cyt	0					620
P43405 UniProt NPD GO	KSYK_HUMAN	Tyrosine-protein kinase SYK (EC 2.7.10.2) (Spleen tyrosine kinase)	0.17	-	cyt	0		T cell receptor complex [IDA]	600085	1XBC	635
P48025 UniProt NPD GO	KSYK_MOUSE	Tyrosine-protein kinase SYK (EC 2.7.10.2) (Spleen tyrosine kinase)	0.17	-	cyt	0		B cell receptor complex [IDA]			629
Q7S9P4 UniProt NPD GO	RU2A_NEUCR	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.17	-	nuc	0	Nucleus (By similarity)				252
Q99KJ0 UniProt NPD GO	UBXD4_MOUSE	UBX domain-containing protein 4	0.17	-	nuc	0					258
Q6C4X5 UniProt NPD GO	HUT1_YARLI	UDP-galactose transporter homolog 1	0.17	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				365
O14179 UniProt NPD GO	YDS3_SCHPO	UPF0023 protein C4F8.03	0.17	-	cyt	0					246
Q9SD33 UniProt NPD GO	U183_ARATH	UPF0183 protein At3g51130	0.17	-	nuc	1					417
Q9C9G6 UniProt NPD GO	U195A_ARATH	UPF0195 protein At1g68310	0.17	-	nuc	0					159

You are viewing entries 55051 to 55100 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.