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
Q13889 UniProt NPD GO	TF2H3_HUMAN	TFIIH basal transcription factor complex p34 subunit (Basic transcription factor 2 34 kDa subunit) ( ...	0.26	-	cyt	0	Nucleus	transcription factor TFIIH complex [NAS]	601750		308
Q91012 UniProt NPD GO	T22D1_CHICK	TSC22 domain family protein 1 (Transforming growth factor beta-1-induced transcript 4 protein) (Regu ...	0.26	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				144
Q15714 UniProt NPD GO	T22D1_HUMAN	TSC22 domain family protein 1 (Transforming growth factor beta-1-induced transcript 4 protein) (Regu ...	0.26	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		607715		144
Q7TQA4 UniProt NPD GO	TR140_MOUSE	Taste receptor type 2 member 140 (T2R140) (Taste receptor type 2 member 40) (T2R40) (T2R8) (T2R13) ( ...	0.26	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			312
Q9JKE7 UniProt NPD GO	T2R41_RAT	Taste receptor type 2 member 41 (T2R41) (T2R12)	0.26	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			308
Q646A1 UniProt NPD GO	T2R50_GORGO	Taste receptor type 2 member 50 (T2R50)	0.26	-	end	7 *	Membrane; multi-pass membrane protein				299
O14095 UniProt NPD GO	YERC_SCHPO	Thioredoxin domain-containing protein C2F3.12c	0.26	-	mit	0					279
Q06441 UniProt NPD GO	TSP4_XENLA	Thrombospondin-4 precursor	0.26	-	nuc	0					955
P36423 UniProt NPD GO	THAS_MOUSE	Thromboxane-A synthase (EC 5.3.99.5) (TXA synthase) (TXS) (TS) (Cytochrome P450 5A1)	0.26	-	end	1 *	Membrane; multi-pass membrane protein				533
P25683 UniProt NPD GO	TX48_DENJA	Toxin S4C8	0.26	-	mit	0	Secreted protein				60
Q7YS70 UniProt NPD GO	MECR_BOVIN	Trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38) (BtNrbf-1) (NRBF-1)	0.26	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			373
P13776 UniProt NPD GO	REP1_ZYGBA	Trans-acting factor B (REP1)	0.26	-	cyt	0					357
Q9AR74 UniProt NPD GO	TCMO_RUTGR	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.26	-	end	0					506
Q7XAQ6 UniProt NPD GO	LAX_ORYSA	Transcription factor LAX PANICLE	0.26	-	cyt	0	Nucleus (Probable)				215
P35189 UniProt NPD GO	TAF14_YEAST	Transcription initiation factor TFIID subunit 14 (TBP-associated factor 14) (TBP-associated factor 3 ...	0.26	-	mit	0	Nucleus	histone acetyltransferase complex [IPI] INO80 complex [IPI] mediator complex [IPI] SWI/SNF complex [IPI] transcription factor TFIID complex [IDA] transcription factor TFIIF complex [IPI]			244
Q9Y5S1 UniProt NPD GO	TRPV2_HUMAN	Transient receptor potential cation channel subfamily V member 2 (TrpV2) (osm-9-like TRP channel 2) ...	0.26	-	end	6	Cell membrane; multi-pass membrane protein (By similarity). Cytoplasm (By similarity). Translocates ...	integral to plasma membrane [TAS]	606676		764
Q3V4Z9 UniProt NPD GO	IF1C_ACOCL	Translation initiation factor IF-1, chloroplast	0.26	-	nuc	0	Plastid; chloroplast				77
Q95GN5 UniProt NPD GO	IF1C_ASACA	Translation initiation factor IF-1, chloroplast	0.26	-	nuc	0	Plastid; chloroplast				77
Q9MS97 UniProt NPD GO	IF3C_GALSU	Translation initiation factor IF-3, chloroplast	0.26	-	nuc	0	Plastid; chloroplast				181
Q91V04 UniProt NPD GO	TRAM1_MOUSE	Translocation-associated membrane protein 1	0.26	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				373
Q924Z5 UniProt NPD GO	TRAM2_MOUSE	Translocation-associated membrane protein 2	0.26	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				370
Q8WW62 UniProt NPD GO	TMED6_HUMAN	Transmembrane emp24 domain-containing protein 6 precursor	0.26	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				240
O14668 UniProt NPD GO	TMG1_HUMAN	Transmembrane gamma-carboxyglutamic acid protein 1 precursor (Proline-rich Gla protein 1) (Proline-r ...	0.26	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	604428		218
Q80X71 UniProt NPD GO	T106B_MOUSE	Transmembrane protein 106B	0.26	-	mit	1	Membrane; single-pass membrane protein (Potential)				275
P00967 UniProt NPD GO	PUR2_DROME	Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase ...	0.26	-	nuc	0					1353
Q9NZC2 UniProt NPD GO	TREM2_HUMAN	Triggering receptor expressed on myeloid cells 2 precursor (Triggering receptor expressed on monocyt ...	0.26	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2, isoform 3: Sec ...		605086		230
Q86XT4 UniProt NPD GO	TRI50_HUMAN	Tripartite motif-containing protein 50	0.26	-	cyt	0					487
P18700 UniProt NPD GO	TBB_STRPU	Tubulin beta chain (Beta tubulin) (Fragment)	0.26	-	cyt	0					292
Q9QXJ0 UniProt NPD GO	TTL_RAT	Tubulin--tyrosine ligase (EC 6.3.2.25) (TTL)	0.26	-	cyt	0					377
P48606 UniProt NPD GO	TBCA_YEAST	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA)	0.26	-	nuc	0		cytoplasm [IDA]		1QSD	106
Q5E951 UniProt NPD GO	TBCB_BOVIN	Tubulin-specific chaperone B (Tubulin folding cofactor B) (Cytoskeleton-associated protein 1) (Cytos ...	0.26	-	mit	0					244
Q5ZI87 UniProt NPD GO	TBCD_CHICK	Tubulin-specific chaperone D (Tubulin-folding cofactor D) (Beta-tubulin cofactor D)	0.26	-	end	0					1019
Q8BYA0 UniProt NPD GO	TBCD_MOUSE	Tubulin-specific chaperone D (Tubulin-folding cofactor D) (Beta-tubulin cofactor D)	0.26	-	end	0					1196
Q9ESE2 UniProt NPD GO	TNF11_RAT	Tumor necrosis factor ligand superfamily member 11 (Receptor activator of nuclear factor kappa B lig ...	0.26	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				318
Q9QYH9 UniProt NPD GO	TNF14_MOUSE	Tumor necrosis factor ligand superfamily member 14 (CD258 antigen) [Contains: Tumor necrosis factor ...	0.26	-	cyt	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	plasma membrane [TAS]			239
Q9USK5 UniProt NPD GO	TIP41_SCHPO	Type 2A phosphatase activator tip41 (PP2A phosphatase activator tip41)	0.26	-	cyt	0	Cytoplasm. Nucleus (By similarity)				252
Q8JI37 UniProt NPD GO	AFP4_PAROL	Type-4 ice-structuring protein precursor (Antifreeze protein type IV)	0.26	-	exc	0	Secreted protein (By similarity)				124
Q95M30 UniProt NPD GO	HCK_MACFA	Tyrosine-protein kinase HCK (EC 2.7.10.2) (p56-HCK) (Hemopoietic cell kinase)	0.26	-	mit	0	Membrane; peripheral membrane protein (By similarity)				503
Q9NY97 UniProt NPD GO	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (Beta3Gn-T1) (BGnT-1) (Be ...	0.26	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	integral to membrane [NAS]	605581		397
O15294 UniProt NPD GO	OGT1_HUMAN	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (EC 2.4.1.-) (O-Glc ...	0.26	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytosol [TAS] nucleus [TAS]	300255	1W3B	1046
P19224 UniProt NPD GO	UD16_HUMAN	UDP-glucuronosyltransferase 1-6 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A6) (UDPGT) (U ...	0.26	-	end	1	Microsome	microsome [NAS]	606431		532
Q9VRJ8 UniProt NPD GO	U139_DROME	UPF0139 protein CG10674	0.26	-	nuc	1 *					108
Q8J0N0 UniProt NPD GO	YCB2_SACPA	UPF0357 protein YCL012C precursor	0.26	-	mit	1 *					133
Q6FSJ2 UniProt NPD GO	UCR7_CANGA	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				128
O24454 UniProt NPD GO	UBP3_ARATH	Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (Ubiquitin thioesterase 3) (Ubiquitin-specific ...	0.26	+	cyt	0	Nucleus				371
Q95LM1 UniProt NPD GO	UBE2U_MACFA	Ubiquitin-conjugating enzyme E2 U (EC 6.3.2.19) (Ubiquitin-protein ligase U) (Ubiquitin carrier prot ...	0.26	-	nuc	0					322
P53152 UniProt NPD GO	MMS2_YEAST	Ubiquitin-conjugating enzyme variant MMS2 (UEV MMS2)	0.26	-	nuc	0		cytoplasm [IDA] nucleus [IDA] ubiquitin conjugating enzyme complex [IPI]		1JAT	137
P39724 UniProt NPD GO	YAE6_YEAST	Uncharacterized bolA-like protein YAL046C	0.26	-	nuc	0					118
P60006 UniProt NPD GO	CK051_HUMAN	Uncharacterized protein C11orf51	0.26	-	nuc	0					121
Q8BPI1 UniProt NPD GO	CN104_MOUSE	Uncharacterized protein C14orf104 homolog	0.26	-	nuc	0					328

You are viewing entries 44751 to 44800 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.