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
Q9I8M6 UniProt NPD GO	SPIB_PALPA	Transcription factor Spi-B-like	0.55	-	nuc	0	Nucleus (Probable)				265
P43273 UniProt NPD GO	TGA2_ARATH	Transcription factor TGA2 (HBP-1b homolog) (AHBP-1b) (AtbZIP20)	0.55	-	nuc	0	Nucleus				330
Q15543 UniProt NPD GO	TAF13_HUMAN	Transcription initiation factor TFIID subunit 13 (Transcription initiation factor TFIID 18 kDa subun ...	0.55	-	cyt	0	Nucleus	transcription factor TFIID complex [TAS]	600774	1BH9	124
P61216 UniProt NPD GO	TAF13_MOUSE	Transcription initiation factor TFIID subunit 13 (Transcription initiation factor TFIID 18 kDa subun ...	0.55	-	cyt	0	Nucleus (By similarity)				124
Q03081 UniProt NPD GO	MET31_YEAST	Transcriptional regulator MET31 (Methionine-requiring protein 31)	0.55	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			177
P31385 UniProt NPD GO	DEP1_YEAST	Transcriptional regulatory protein DEP1	0.55	-	nuc	0	Cytoplasm. Nucleus	nucleus [IC]			420
P56094 UniProt NPD GO	TUP1_KLULA	Transcriptional repressor TUP1	0.55	-	nuc	0					682
Q6R5A3 UniProt NPD GO	TRPV1_CAVPO	Transient receptor potential cation channel subfamily V member 1 (TrpV1) (osm-9-like TRP channel 1) ...	0.55	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				839
P03974 UniProt NPD GO	TERA_PIG	Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)-ATPase p97 subunit) (Valosin-cont ...	0.55	+	cyt	0	Cytoplasm. Nucleus				805
Q6B8N5 UniProt NPD GO	IF3C_GRATL	Translation initiation factor IF-3, chloroplast	0.55	-	nuc	0	Plastid; chloroplast				181
P43307 UniProt NPD GO	SSRA_HUMAN	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.55	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum [TAS] integral to membrane [TAS]	600868		286
P16967 UniProt NPD GO	SSRA_CANFA	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.55	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				286
Q5E9I3 UniProt NPD GO	TMM10_BOVIN	Transmembrane protein 10	0.55	-	nuc	1 *	Membrane; single-pass membrane protein (By similarity)				142
Q29102 UniProt NPD GO	TMM10_PIG	Transmembrane protein 10 (Transmembrane protein sp83.5)	0.55	-	nuc	1 *	Isoform 1: Cell membrane; single-pass membrane protein. Isoform 2: Cytoplasm (Probable)				142
Q1XHT8 UniProt NPD GO	TRI40_PANTR	Tripartite motif-containing protein 40	0.55	-	nuc	0					229
P25805 UniProt NPD GO	CYSP_PLAFA	Trophozoite cysteine proteinase precursor (EC 3.4.22.-) (TCP)	0.55	-	nuc	1 *					569
Q23758 UniProt NPD GO	TPM_CLOSI	Tropomyosin	0.55	-	nuc	0					284
Q95PU1 UniProt NPD GO	TPM_ECHMU	Tropomyosin	0.55	-	nuc	0					284
P06754 UniProt NPD GO	TPM1_DROME	Tropomyosin 1, isoforms 9A/A/B (Tropomyosin II) (Cytoskeletal tropomyosin)	0.55	-	nuc	0	Isoform 9A: Cytoplasm				339
Q8IWU9 UniProt NPD GO	TPH2_HUMAN	Tryptophan 5-hydroxylase 2 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 2) (Neuronal tryptophan hydrox ...	0.55	-	cyt	0			608516		490
Q9NS68 UniProt NPD GO	TNR19_HUMAN	Tumor necrosis factor receptor superfamily member 19 precursor (Toxicity and JNK inducer) (TRADE)	0.55	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	integral to membrane [NAS]	606122		423
Q8BX43 UniProt NPD GO	TR19L_MOUSE	Tumor necrosis factor receptor superfamily member 19L precursor	0.55	-	exc	2 *	Membrane; single-pass type I membrane protein (Probable)				436
Q56JV6 UniProt NPD GO	TWF1_BOVIN	Twinfilin-1	0.55	-	nuc	0	Cytoplasm. Diffuse cytoplasmic localization with perinuclear and G-actin-rich cortical actin structu ...				350
P24529 UniProt NPD GO	TY3H_MOUSE	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.55	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			498
Q9NV31 UniProt NPD GO	IMP3_HUMAN	U3 small nucleolar ribonucleoprotein protein IMP3 (U3 snoRNP protein IMP3) (BRMS2)	0.55	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA]		2CQJ	184
Q8C5U9 UniProt NPD GO	UBQL3_MOUSE	Ubiquilin-3	0.55	-	nuc	0					658
P38150 UniProt NPD GO	YB9Z_YEAST	Uncharacterized deaminase YBR284W (EC 3.5.4.-)	0.55	-	cyt	0					797
P43618 UniProt NPD GO	YFL6_YEAST	Uncharacterized protein YFR046C	0.55	-	nuc	0		kinetochore [IDA] nucleus [IDA]			361
P53200 UniProt NPD GO	YG11_YEAST	Uncharacterized protein YGR001C	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA]			248
P53210 UniProt NPD GO	YG1B_YEAST	Uncharacterized protein YGR017W	0.55	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			297
Q96PQ0 UniProt NPD GO	SORC2_HUMAN	VPS10 domain-containing receptor SorCS2 precursor	0.55	-	end	1	Membrane; single-pass type I membrane protein	membrane [NAS]	606284	1WGO	1159
O14265 UniProt NPD GO	VATH_SCHPO	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H) ...	0.55	-	cyt	0					450
Q9H267 UniProt NPD GO	VP33B_HUMAN	Vacuolar protein sorting 33B (hVPS33B)	0.55	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; p ...		608552		617
Q04272 UniProt NPD GO	VPS20_YEAST	Vacuolar protein sorting protein 20 (Amino acid sensor-independent protein 10) (Charged multivesicul ...	0.55	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein. Vacuole; vacuolar membrane; peripheral me ...	cytoplasm [IDA] ESCRT III complex [IDA]			220
Q9URZ5 UniProt NPD GO	VPS1_SCHPO	Vacuolar sorting protein 1	0.55	-	cyt	0					678
P26330 UniProt NPD GO	VSI5_TRYBB	Variant surface glycoprotein ILTAT 1.25 precursor (VSG)	0.55	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				507
O35757 UniProt NPD GO	VEGFC_RAT	Vascular endothelial growth factor C precursor (VEGF-C) (Vascular endothelial growth factor-related ...	0.55	-	exc	0	Secreted protein				415
P00980 UniProt NPD GO	IVBII_DENAN	Venom basic protease inhibitor 1 homolog (Alpha-dendrotoxin) (Alpha-DTX) (Toxin C13S2C3)	0.55	-	nuc	0	Secreted protein			1DTX	59
P54287 UniProt NPD GO	CACB3_RAT	Voltage-dependent L-type calcium channel subunit beta-3 (CAB3) (Calcium channel voltage-dependent su ...	0.55	-	nuc	0		voltage-gated calcium channel complex [IDA]		1VYU	484
P91645 UniProt NPD GO	CAC1A_DROME	Voltage-dependent calcium channel type A alpha-1 subunit (Cacophony protein) (Nightblind A protein) ...	0.55	+	end	19 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA] voltage-gated calcium channel complex [NAS]			1851
Q8TCV5 UniProt NPD GO	WFDC5_HUMAN	WAP four-disulfide core domain protein 5 precursor (Putative protease inhibitor WAP1)	0.55	-	exc	0	Secreted protein (Potential)				224
Q8BHD1 UniProt NPD GO	WD51B_MOUSE	WD repeat protein 51B	0.55	-	nuc	0					476
P53851 UniProt NPD GO	YNZ3_YEAST	WD repeat protein YNL253W	0.55	-	nuc	0		transcription export complex [IPI]			422
Q9NP60 UniProt NPD GO	IRPL2_HUMAN	X-linked interleukin-1 receptor accessory protein-like 2 precursor (IL1RAPL-2-related protein) (Inte ...	0.55	+	end	1	Membrane; single-pass type I membrane protein		300277		686
P53169 UniProt NPD GO	YBP2_YEAST	YAP1-binding protein 2	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA]			641
Q7Z739 UniProt NPD GO	YTHD3_HUMAN	YTH domain protein 3	0.55	-	nuc	0					585
Q5RFL8 UniProt NPD GO	YTHD3_PONPY	YTH domain protein 3	0.55	-	nuc	0					585
O76080 UniProt NPD GO	Z20D2_HUMAN	Zinc finger A20 domain-containing protein 2 (Zinc finger protein 216)	0.55	-	nuc	0			604761		213
Q8N5A5 UniProt NPD GO	ZGPAT_HUMAN	Zinc finger CCCH-type with G patch domain protein (Zinc finger CCCH domain-containing protein 9)	0.55	-	nuc	0					531
Q92010 UniProt NPD GO	ZF161_CHICK	Zinc finger protein 161 homolog (Zfp-161) (Zinc finger protein 5) (ZF5)	0.55	-	nuc	0	Nucleus (By similarity)				448

You are viewing entries 22251 to 22300 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.