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
Q9WVB2 UniProt NPD GO	TLE2_MOUSE	Transducin-like enhancer protein 2	0.52	-	nuc	0	Nucleus				767
Q04638 UniProt NPD GO	ITT1_YEAST	Translation termination inhibitor protein ITT1	0.52	-	end	0					464
Q75UR0 UniProt NPD GO	TM16E_MOUSE	Transmembrane protein 16E (Gnathodiaphyseal dysplasia 1 protein homolog)	0.52	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Co-localized wit ...				904
O01479 UniProt NPD GO	TMOD_CAEEL	Tropomodulin (Tmod-like protein) (cTmd1)	0.52	-	nuc	0				1PGV	392
Q7Z9Z2 UniProt NPD GO	TBG_COPCI	Tubulin gamma chain (Gamma tubulin)	0.52	+	cyt	0					453
P46670 UniProt NPD GO	CIN2_YEAST	Tubulin-folding cofactor C (Protein CIN2) (Chromosome instability protein 2)	0.52	-	nuc	0					268
Q9NNX1 UniProt NPD GO	TUFT1_HUMAN	Tuftelin	0.52	-	nuc	0	Secreted protein (By similarity). Secreted at a very early stage of enamel formation, concentrated a ...	extracellular region [NAS]	600087		390
P51867 UniProt NPD GO	TNR6_BOVIN	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.52	-	nuc	1	Membrane; single-pass type I membrane protein				323
Q91YR1 UniProt NPD GO	TWF1_MOUSE	Twinfilin-1 (Protein A6)	0.52	-	nuc	0	Cytoplasm. Diffuse cytoplasmic localization with perinuclear and G-actin-rich cortical actin structu ...	actin cytoskeleton [IDA]		1M4J	350
Q12792 UniProt NPD GO	TWF1_HUMAN	Twinfilin-1 (Protein A6) (Protein tyrosine kinase 9)	0.52	-	nuc	0	Cytoplasm. Diffuse cytoplasmic localization with perinuclear and G-actin-rich cortical actin structu ...	actin cytoskeleton [ISS]			368
P11344 UniProt NPD GO	TYRO_MOUSE	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase) (Albino locus protein)	0.52	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein	integral to membrane [TAS] melanosome [IDA]			533
P43403 UniProt NPD GO	ZAP70_HUMAN	Tyrosine-protein kinase ZAP-70 (EC 2.7.10.2) (70 kDa zeta-associated protein) (Syk-related tyrosine ...	0.52	-	mit	0		cytoplasm [TAS] T cell receptor complex [IDA]	176947	1U59	619
Q13308 UniProt NPD GO	PTK7_HUMAN	Tyrosine-protein kinase-like 7 precursor (Colon carcinoma kinase 4) (CCK-4)	0.52	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601890		1070
P28199 UniProt NPD GO	PTP7_STYPL	Tyrosine-protein phosphatase 7 (EC 3.1.3.48) (Fragment)	0.52	-	nuc	0					112
O13823 UniProt NPD GO	IMP4_SCHPO	U3 small nucleolar ribonucleoprotein protein imp4 (U3 snoRNP protein imp4)	0.52	-	nuc	0	Nucleus; nucleolus (By similarity)				289
Q9DAW6 UniProt NPD GO	PRP4_MOUSE	U4/U6 small nuclear ribonucleoprotein Prp4 (U4/U6 snRNP 60 kDa protein) (WD splicing factor Prp4)	0.52	-	mit	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...				521
P40070 UniProt NPD GO	LSM4_YEAST	U6 snRNA-associated Sm-like protein LSm4	0.52	-	nuc	0	Nucleus. Cytoplasm	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			187
P38349 UniProt NPD GO	UBX7_YEAST	UBX domain-containing protein 7	0.52	-	nuc	0	Endoplasmic reticulum	endoplasmic reticulum [IDA] nuclear envelope [IDA]			436
O74933 UniProt NPD GO	UAP1_CANAL	UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)	0.52	-	nuc	0	Cytoplasm (By similarity)				486
Q8C4X7 UniProt NPD GO	U258_MOUSE	UPF0258 protein	0.52	-	nuc	1					151
Q14694 UniProt NPD GO	UBP10_HUMAN	Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.1.2.15) (Ubiquitin thioesterase 10) (Ubiquitin-specif ...	0.52	+	nuc	0			609818		798
Q05086 UniProt NPD GO	UBE3A_HUMAN	Ubiquitin-protein ligase E3A (EC 6.3.2.-) (E6AP ubiquitin-protein ligase) (Oncogenic protein-associa ...	0.52	-	nuc	0	Nucleus (Probable)		105830	1EQX	875
O08759 UniProt NPD GO	UBE3A_MOUSE	Ubiquitin-protein ligase E3A (EC 6.3.2.-) (Oncogenic protein-associated protein E6-AP)	0.52	-	cyt	0	Cytoplasm. Nucleus	cytosol [IDA] nucleus [IDA]			885
Q9NX94 UniProt NPD GO	CJ026_HUMAN	Uncharacterized protein C10orf26	0.52	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				342
Q8BGW2 UniProt NPD GO	CJ026_MOUSE	Uncharacterized protein C10orf26 homolog	0.52	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				348
Q9H4H8 UniProt NPD GO	CT129_HUMAN	Uncharacterized protein C20orf129	0.52	-	nuc	0					585
P28817 UniProt NPD GO	YD036_YEAST	Uncharacterized protein YDR036C	0.52	-	mit	0		mitochondrion [IDA]			500
P53273 UniProt NPD GO	YG35_YEAST	Uncharacterized protein YGR125W	0.52	-	end	10	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			1036
P53903 UniProt NPD GO	YNO9_YEAST	Uncharacterized protein YNL149C	0.52	+	cyt	1 *	Endoplasmic reticulum	endoplasmic reticulum [IDA] nuclear envelope [IDA]			128
Q9Y2C2 UniProt NPD GO	UST_HUMAN	Uronyl 2-sulfotransferase (EC 2.8.2.-)	0.52	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [TAS]			406
Q91830 UniProt NPD GO	RAG2_XENLA	V(D)J recombination-activating protein 2 (RAG-2)	0.52	+	mit	0	Nucleus				520
P32912 UniProt NPD GO	VAM7_YEAST	Vacuolar morphogenesis protein 7	0.52	-	nuc	0	Vacuole	vacuolar membrane (sensu Fungi) [IDA]		1KMD	316
Q96QK1 UniProt NPD GO	VPS35_HUMAN	Vacuolar protein sorting 35 (Vesicle protein sorting 35) (hVPS35) (Maternal-embryonic 3)	0.52	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein	cytosol [IDA]	606931		796
P32319 UniProt NPD GO	PEP1_YEAST	Vacuolar protein sorting/targeting protein PEP1 precursor (Vacuolar carboxypeptidase sorting recepto ...	0.52	-	end	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...	Golgi apparatus [TAS]			1579
P20947 UniProt NPD GO	VSWB_TRYBR	Variant surface glycoprotein WRATAT B precursor (VSG)	0.52	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				487
P83906 UniProt NPD GO	VEGFA_BITGA	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.52	-	nuc	0	Secreted protein				191
Q9DEZ9 UniProt NPD GO	NGFV_CRODU	Venom nerve growth factor precursor (vNGF)	0.52	-	exc	0	Secreted protein				241
Q9SEL5 UniProt NPD GO	VTI12_ARATH	Vesicle transport v-SNARE 12 (AtVTI12) (Vesicle transport v-SNARE protein VTI1b) (Vesicle soluble NS ...	0.52	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				222
Q6BVM4 UniProt NPD GO	BOS1_DEBHA	Vesicular transport protein BOS1	0.52	-	cyt	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein (By similarity). Secretor ...				229
P34732 UniProt NPD GO	SEC18_CANAL	Vesicular-fusion protein SEC18	0.52	-	mit	0	Cytoplasm				794
O88496 UniProt NPD GO	VKGC_RAT	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.52	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
Q5E9I8 UniProt NPD GO	WDR23_BOVIN	WD repeat protein 23	0.52	-	nuc	0					546
Q8TEB1 UniProt NPD GO	WDR23_HUMAN	WD repeat protein 23	0.52	-	nuc	0					546
P38149 UniProt NPD GO	YB9X_YEAST	WD repeat protein YBR281C	0.52	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			878
Q9P202 UniProt NPD GO	WHRN_HUMAN	Whirlin (Autosomal recessive deafness type 31 protein)	0.52	-	nuc	0	Cytoplasm. Detected at the level of stereocilia in inner hair cells and in outer hair cells in the c ...		607084	1UFX	907
Q60595 UniProt NPD GO	XL3A_MOUSE	X-linked lymphocyte-regulated protein 3A	0.52	-	nuc	0					226
Q49LS1 UniProt NPD GO	XKR7_PANTR	XK-related protein 7	0.52	-	end	6	Membrane; multi-pass membrane protein (Potential)				579
Q9CQK1 UniProt NPD GO	ZNHI3_MOUSE	Zinc finger HIT domain-containing protein 3 (Thyroid receptor-interacting protein 3) (TRIP-3) (Thyro ...	0.52	-	nuc	0					151
Q8NCN2 UniProt NPD GO	ZBT34_HUMAN	Zinc finger and BTB domain-containing protein 34	0.52	-	nuc	0	Nucleus (Probable)				500
Q42485 UniProt NPD GO	ZFP1_ARATH	Zinc finger protein 1	0.52	-	nuc	0					228

You are viewing entries 24051 to 24100 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.