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
P34233 UniProt NPD GO	ASH1_YEAST	Transcriptional regulatory protein ASH1 (Daughter cells HO repressor protein)	0.83	-	nuc	0	Nucleus. Preferentially accumulates in daughter cell nuclei at the end of anaphase	histone deacetylase complex [IPI] nucleus [IDA]			588
O94876 UniProt NPD GO	TMCC1_HUMAN	Transmembrane and coiled-coil domains protein 1	0.83	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				653
Q8BHE4 UniProt NPD GO	TM108_MOUSE	Transmembrane protein 108 precursor	0.83	-	exc	2 *	Membrane; single-pass type I membrane protein				574
Q8MIH1 UniProt NPD GO	TWST1_CALJA	Twist-related protein 1	0.83	-	nuc	0	Nucleus (By similarity)				203
Q8MI06 UniProt NPD GO	TWST1_GORGO	Twist-related protein 1	0.83	-	nuc	0	Nucleus (By similarity)				203
Q8MIE7 UniProt NPD GO	TWST1_HYLCO	Twist-related protein 1	0.83	-	nuc	0	Nucleus (By similarity)				204
Q15672 UniProt NPD GO	TWST1_HUMAN	Twist-related protein 1 (H-twist)	0.83	-	nuc	0	Nucleus		601622		202
P26687 UniProt NPD GO	TWST1_MOUSE	Twist-related protein 1 (M-twist)	0.83	-	nuc	0	Nucleus	nucleus [NAS]			206
P97831 UniProt NPD GO	TWST2_RAT	Twist-related protein 2	0.83	-	nuc	0	Nucleus (By similarity). Mainly nuclear during embryonic development. Cytoplasm (By similarity). Cyt ...	cytoplasm [ISS] nucleus [ISS]			160
Q8WVJ9 UniProt NPD GO	TWST2_HUMAN	Twist-related protein 2 (Dermis expressed protein 1) (Dermo-1)	0.83	-	nuc	0	Nucleus. Mainly nuclear during embryonic development. Cytoplasm. Cytoplasmic in adult tissues	cytoplasm [IDA] nucleus [IDA]	607556		160
Q9D030 UniProt NPD GO	TWST2_MOUSE	Twist-related protein 2 (Dermis expressed protein 1) (Dermo-1)	0.83	-	nuc	0	Nucleus. Mainly nuclear during embryonic development. Cytoplasm. Cytoplasmic in adult tissues	transcription factor complex [IPI]			160
Q02354 UniProt NPD GO	UTP6_YEAST	U3 small nucleolar RNA-associated protein 6 (U3 snoRNA-associated protein 6)	0.83	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			440
Q8BG34 UniProt NPD GO	UBXD3_MOUSE	UBX domain-containing protein 3	0.83	-	nuc	0					277
Q80XC3 UniProt NPD GO	US6NL_MOUSE	USP6 N-terminal-like protein	0.83	-	nuc	0					819
Q9UPT9 UniProt NPD GO	UBP22_HUMAN	Ubiquitin carboxyl-terminal hydrolase 22 (EC 3.1.2.15) (Ubiquitin thioesterase 22) (Ubiquitin-specif ...	0.83	-	nuc	0					525
Q9CQJ4 UniProt NPD GO	RING2_MOUSE	Ubiquitin ligase protein RING2 (EC 6.3.2.-) (RING finger protein 2) (RING finger protein 1B) (RING1b ...	0.83	-	nuc	0	Nucleus. Enriched on inactive X chromosome (Xi) in female trophoblast stem (TS) cells as well as dif ...	nuclear body [IDA] nucleus [IDA]		2CKL	336
Q5R9J5 UniProt NPD GO	RING2_PONPY	Ubiquitin ligase protein RING2 (EC 6.3.2.-) (RING finger protein 2) (RING finger protein 1B) (RING1b ...	0.83	-	nuc	0	Nucleus. Enriched on inactive X chromosome (Xi) in female trophoblast stem (TS) cells as well as dif ...				336
Q99496 UniProt NPD GO	RING2_HUMAN	Ubiquitin ligase protein RING2 (EC 6.3.2.-) (RING finger protein 2) (RING finger protein 1B) (RING1b ...	0.83	-	nuc	0	Nucleus. Enriched on inactive X chromosome (Xi) in female trophoblast stem (TS) cells as well as dif ...		608985		336
Q8VDF2 UniProt NPD GO	UHRF1_MOUSE	Ubiquitin-like PHD and RING finger domain-containing protein 1 (EC 6.3.2.-) (Ubiquitin-like-containi ...	0.83	-	nuc	0	Nucleus	nucleus [TAS]			782
Q07457 UniProt NPD GO	BRE1_YEAST	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-) (Brefeldin A-sensitivity protein 1)	0.83	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			700
O60152 UniProt NPD GO	UBR1_SCHPO	Ubiquitin-protein ligase E3 component N-recognin-1 (EC 6.-.-.-) (N-end-recognizing protein)	0.83	-	nuc	0					1958
Q9H972 UniProt NPD GO	CN093_HUMAN	Uncharacterized protein C14orf93 precursor	0.83	-	nuc	0					538
Q8ND99 UniProt NPD GO	CS016_HUMAN	Uncharacterized protein C19orf16	0.83	-	nuc	0					567
Q8BLN6 UniProt NPD GO	CB021_MOUSE	Uncharacterized protein C2orf21 homolog	0.83	-	nuc	0					394
P38243 UniProt NPD GO	YBS1_YEAST	Uncharacterized protein YBR071W	0.83	-	mit	0		cytoplasm [IDA]			211
P40021 UniProt NPD GO	YEM3_YEAST	Uncharacterized protein YER033C	0.83	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			1076
P43586 UniProt NPD GO	YFH1_YEAST	Uncharacterized protein YFR001W	0.83	+	nuc	0		nucleus [IDA]			204
Q06152 UniProt NPD GO	YL271_YEAST	Uncharacterized protein YLR271W	0.83	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			274
P53743 UniProt NPD GO	YN8V_YEAST	Uncharacterized protein YNR054C	0.83	-	nuc	0		cytoplasm [IDA] nucleolus [IDA] small nucleolar ribonucleoprotein complex [IDA]			316
Q12275 UniProt NPD GO	YO093_YEAST	Uncharacterized protein YOR093C	0.83	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				1648
Q12108 UniProt NPD GO	YO118_YEAST	Uncharacterized protein YOR118W	0.83	-	nuc	0	Cytoplasm	cytoplasm [IDA]			567
Q08748 UniProt NPD GO	YO296_YEAST	Uncharacterized protein YOR296W	0.83	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1289
Q9GL21 UniProt NPD GO	UACA_CANFA	Uveal autoantigen with coiled-coil domains and ankyrin repeats protein	0.83	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Expressed diffusely in cytoplasm (By similarity) ...				1415
O95670 UniProt NPD GO	VATG2_HUMAN	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.83	-	nuc	0			606853		118
P47061 UniProt NPD GO	VPS53_YEAST	Vacuolar protein sorting protein 53	0.83	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	cytoplasm [IDA] GARP complex [IPI] Golgi apparatus [IDA]			822
P50552 UniProt NPD GO	VASP_HUMAN	Vasodilator-stimulated phosphoprotein (VASP)	0.83	-	nuc	0	Cytoplasm. Targeted to stress fibers and focal adhesions through interaction with a number of protei ...	actin cytoskeleton [TAS]	601703	1USE	379
P09801 UniProt NPD GO	VCLB_GOSHI	Vicilin C72 precursor (Alpha-globulin B)	0.83	-	exc	1 *	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				588
Q28037 UniProt NPD GO	VDR_BOVIN	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.83	+	nuc	0	Nucleus				424
O42392 UniProt NPD GO	VDR_CHICK	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.83	+	nuc	0	Nucleus				451
P11473 UniProt NPD GO	VDR_HUMAN	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.83	+	nuc	0	Nucleus		277440	1YNW	427
P48281 UniProt NPD GO	VDR_MOUSE	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.83	+	nuc	0	Nucleus				422
P22002 UniProt NPD GO	CAC1C_RAT	Voltage-dependent L-type calcium channel subunit alpha-1C (Voltage-gated calcium channel subunit alp ...	0.83	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]		1VYT	2169
P54282 UniProt NPD GO	CAC1A_RAT	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage-gated calcium channel subunit a ...	0.83	+	end	17	Membrane; multi-pass membrane protein	integral to membrane [ISS] plasma membrane [IDA] voltage-gated calcium channel complex [TAS]			2212
Q5TJE7 UniProt NPD GO	WDR46_CANFA	WD repeat protein 46	0.83	+	nuc	0					612
Q9LM84 UniProt NPD GO	WOX14_ARATH	WUSCHEL-related homeobox 14 (Homeodomain protein PALE-2) (AtPALE2)	0.83	+	nuc	0	Nucleus (By similarity)				211
Q8H1D2 UniProt NPD GO	WOX5_ARATH	WUSCHEL-related homeobox 5	0.83	-	nuc	0	Nucleus (By similarity)				182
Q8IV90 UniProt NPD GO	WASF4_HUMAN	Wiskott-Aldrich syndrome protein family member 4 (WASP-family protein member 4)	0.83	+	nuc	0					625
P24088 UniProt NPD GO	YRF11_YEAST	Y'helicase protein 1 copies 1/5/8 (EC 3.6.1.-)	0.83	+	nuc	0					1796
P53345 UniProt NPD GO	YRF13_YEAST	Y'helicase protein 1 copies 3/7 (EC 3.6.1.-)	0.83	+	vac	0					1859
P53819 UniProt NPD GO	YRF16_YEAST	Y'helicase protein 1 copy 6 (EC 3.6.1.-)	0.83	+	vac	0					1859

You are viewing entries 7651 to 7700 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.