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
Q863A2 UniProt NPD GO	TBX2_CANFA	T-box transcription factor TBX2 (T-box protein 2)	0.71	-	nuc	0	Nucleus (Potential)				702
Q9XS78 UniProt NPD GO	CD4_DELLE	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.71	-	exc	1	Membrane; single-pass type I membrane protein				455
Q3B7U2 UniProt NPD GO	TAF1A_RAT	TATA box-binding protein-associated factor RNA polymerase I subunit A (TATA box-binding protein-asso ...	0.71	-	cyt	0	Nucleus (By similarity)				453
Q960E8 UniProt NPD GO	TF2H1_DROME	TFIIH basal transcription factor complex subunit 1	0.71	-	nuc	0	Nucleus (By similarity)				585
Q6AYM2 UniProt NPD GO	TEKT2_RAT	Tektin-2 (Testicular tektin) (Tektin-t)	0.71	-	nuc	0					430
Q8IWB9 UniProt NPD GO	TEX2_HUMAN	Testis-expressed sequence 2 protein	0.71	-	end	2	Membrane; multi-pass membrane protein (Potential)				1127
O14598 UniProt NPD GO	VCY1_HUMAN	Testis-specific basic protein Y 1 (Variably charged protein Y)	0.71	-	nuc	0			400012		125
Q99614 UniProt NPD GO	TTC1_HUMAN	Tetratricopeptide repeat protein 1 (TPR repeat protein 1)	0.71	-	nuc	0			601963		292
P18113 UniProt NPD GO	THB1_RAT	Thyroid hormone receptor beta-1	0.71	+	nuc	0	Nucleus	nucleus [TAS]			461
Q5PQX1 UniProt NPD GO	TOIP1_RAT	Torsin-1A-interacting protein 1 (Lamina-associated polypeptide 1B) (Lamina-associated polypeptide 1C ...	0.71	-	nuc	0	Nucleus; nuclear inner membrane; single-pass membrane protein				583
Q62314 UniProt NPD GO	TGON2_MOUSE	Trans-Golgi network integral membrane protein 2 precursor (TGN38B)	0.71	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Golgi apparatus; trans-Golgi net ...	trans-Golgi network transport vesicle [IDA]			363
Q80V24 UniProt NPD GO	VGLL4_MOUSE	Transcription cofactor vestigial-like protein 4 (Vgl-4)	0.71	-	nuc	0	Nucleus (By similarity)				287
Q3UNW5 UniProt NPD GO	TF2L1_MOUSE	Transcription factor CP2-like protein 1 (CP2-related transcriptional repressor 1) (CRTR-1)	0.71	-	nuc	0	Nucleus				478
P35429 UniProt NPD GO	HES2_RAT	Transcription factor HES-2 (Hairy and enhancer of split 2)	0.71	-	nuc	0	Nucleus	nucleus [TAS]			157
Q24266 UniProt NPD GO	BTD_DROME	Transcription factor btd (Protein buttonhead)	0.71	-	nuc	0	Nucleus (By similarity)				644
P18888 UniProt NPD GO	SNF6_YEAST	Transcription regulatory protein SNF6 (SWI/SNF complex component SNF6)	0.71	+	nuc	0	Nucleus	SWI/SNF complex [TAS]			332
Q15562 UniProt NPD GO	TEAD2_HUMAN	Transcriptional enhancer factor TEF-4 (TEA domain family member 2) (TEAD-2)	0.71	-	nuc	0	Nucleus	nucleus [NAS]	601729		447
P09533 UniProt NPD GO	TGFB1_CERAE	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.71	-	exc	0	Secreted protein				390
Q94KR9 UniProt NPD GO	IF1C_LYCES	Translation initiation factor IF-1, chloroplast precursor	0.71	-	nuc	0	Plastid; chloroplast (By similarity)				156
Q12000 UniProt NPD GO	TMA46_YEAST	Translation machinery-associated protein 46	0.71	-	nuc	0	Cytoplasm	cytoplasm [IDA]			345
Q9QZE7 UniProt NPD GO	TSNAX_MOUSE	Translin-associated protein X (Translin-associated factor X)	0.71	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA]			290
P15533 UniProt NPD GO	TRI30_MOUSE	Tripartite motif-containing protein 30 (Down regulatory protein of interleukin 2 receptor)	0.71	-	nuc	0	Nucleus	cytoplasm [IDA]			496
P27672 UniProt NPD GO	TNNI3_COTJA	Troponin I, cardiac muscle (Cardiac troponin I)	0.71	-	nuc	0					207
Q5PYI0 UniProt NPD GO	TNNI3_HORSE	Troponin I, cardiac muscle (Cardiac troponin I)	0.71	-	nuc	0					204
Q9Y882 UniProt NPD GO	TBG_SCHJP	Tubulin gamma chain (Gamma tubulin)	0.71	+	cyt	0					446
P23257 UniProt NPD GO	TBG1_DROME	Tubulin gamma-1 chain (Gamma-1 tubulin)	0.71	+	nuc	0		gamma-tubulin small complex [IPI]			475
P23258 UniProt NPD GO	TBG1_HUMAN	Tubulin gamma-1 chain (Gamma-1 tubulin) (Gamma-tubulin complex component 1) (GCP-1)	0.71	+	cyt	0	Centrosome	centrosome [TAS] condensed nuclear chromosome [ISS] cytoplasm [IDA] gamma-tubulin complex [TAS] microtubule [TAS] polar microtubule [IDA] spindle pole body [TAS]	191135	1Z5W	451
Q60769 UniProt NPD GO	TNAP3_MOUSE	Tumor necrosis factor, alpha-induced protein 3 (EC 3.-.-.-) (Putative DNA-binding protein A20) (Zinc ...	0.71	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA]			775
O74345 UniProt NPD GO	UCP3_SCHPO	UBA domain-containing protein 3	0.71	-	nuc	0					601
O94685 UniProt NPD GO	UCP8_SCHPO	UBA domain-containing protein 8	0.71	-	nuc	0					884
P53741 UniProt NPD GO	BRE5_YEAST	UBP3-associated protein BRE5 (Brefeldin-A sensitivity protein 5)	0.71	-	nuc	0		cytoplasm [IDA]		1ZX2	515
Q9QZ49 UniProt NPD GO	UBXD6_MOUSE	UBX domain-containing protein 6 (Rep-8 protein) (Reproduction 8 protein)	0.71	+	exc	2 *				2CR5	277
Q9HGM7 UniProt NPD GO	YW04_SCHPO	UPF0171 protein C543.04	0.71	-	mit	0					585
Q9VSU7 UniProt NPD GO	USE1_DROME	USE1-like protein	0.71	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum [ISS]			250
P33202 UniProt NPD GO	UFD4_YEAST	Ubiquitin fusion degradation protein 4 (UB fusion protein 4)	0.71	-	mit	0		cytoplasm [IPI] mitochondrion [IDA]			1483
P38290 UniProt NPD GO	UBS1_YEAST	Ubiquitin-conjugating enzyme suppressor 1	0.71	-	nuc	0		nucleus [IDA]			277
Q810L3 UniProt NPD GO	CHFR_MOUSE	Ubiquitin-protein ligase CHFR (EC 6.3.2.-) (Checkpoint with forkhead and RING finger domains protein ...	0.71	-	nuc	0	Nucleus (By similarity)				664
Q9R189 UniProt NPD GO	UN13D_RAT	Unc-13 homolog D (Munc13-4)	0.71	+	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Colocalizes with c ...				1088
Q9H8Y1 UniProt NPD GO	CN115_HUMAN	Uncharacterized protein C14orf115	0.71	-	cyt	0					702
Q80WW9 UniProt NPD GO	CT116_MOUSE	Uncharacterized protein C20orf116 homolog precursor	0.71	-	exc	1 *	Secreted protein (Potential)			1WI9	315
Q9D7I8 UniProt NPD GO	CT129_MOUSE	Uncharacterized protein C20orf129 homolog	0.71	-	nuc	0					585
Q5TEA3 UniProt NPD GO	CT194_HUMAN	Uncharacterized protein C20orf194	0.71	-	nuc	0					1177
O13859 UniProt NPD GO	YEX8_SCHPO	Uncharacterized protein SPAC1A6.08c	0.71	-	nuc	0					285
P46949 UniProt NPD GO	YG4A_YEAST	Uncharacterized protein YGR196C	0.71	-	nuc	0		cytoplasm [IDA]			817
P53309 UniProt NPD GO	YG54_YEAST	Uncharacterized protein YGR241C	0.71	-	nuc	0		actin cortical patch [IDA]			568
P40456 UniProt NPD GO	YI151_YEAST	Uncharacterized protein YIL151C	0.71	-	mit	0					1118
P53718 UniProt NPD GO	YN85_YEAST	Uncharacterized protein YNR009W	0.71	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			249
P53723 UniProt NPD GO	YN8B_YEAST	Uncharacterized protein YNR021W	0.71	-	mit	1 *	Endoplasmic reticulum	endoplasmic reticulum [IDA]			403
Q2QI47 UniProt NPD GO	USH2A_MOUSE	Usherin precursor (Usher syndrome type-2A protein homolog) (Usher syndrome type IIa protein homolog) ...	0.71	+	exc	2 *	Membrane; single-pass type I membrane protein. Probable component of the interstereocilia ankle link ...				5193
P38959 UniProt NPD GO	VPS41_YEAST	Vacuolar assembly protein VPS41 (Vacuolar morphogenesis protein 2)	0.71	+	nuc	0		endosome [IDA] HOPS complex [IPI] vacuole (sensu Fungi) [IDA]			992

You are viewing entries 13551 to 13600 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.